Mercurial > repos > rnateam > graphprot_predict_profile

annotate gplib.py @ 3:9a83a84a25a7 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
author bgruening
date Wed, 27 Jan 2021 19:27:12 +0000
parents adcc4c457c3c
children 58ebf089377e
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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2 import gzip
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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3 import random
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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4 import re
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9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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5 import statistics
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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6 import subprocess
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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7 from distutils.spawn import find_executable
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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10 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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12 Run doctests:
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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14 python3 -m doctest gplib.py
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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17 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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20 ###############################################################################
1
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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22 def graphprot_predictions_get_median(predictions_file):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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23 """
3
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24 Given a GraphProt .predictions file, read in site scores and return
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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25 the median value.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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27 >>> test_file = "test-data/test.predictions"
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28 >>> graphprot_predictions_get_median(test_file)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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29 0.571673
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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31 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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32 # Site scores list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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33 sc_list = []
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34 with open(predictions_file) as f:
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35 for line in f:
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36 cols = line.strip().split("\t")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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37 score = float(cols[2])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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38 sc_list.append(score)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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39 f.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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40 # Return the median.
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41 return statistics.median(sc_list)
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44 ###############################################################################
1
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46 def graphprot_profile_get_tsm(profile_file,
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47 profile_type="profile",
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48 avg_profile_extlr=5):
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49
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50 """
3
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51 Given a GraphProt .profile file, extract for each site (identified by
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52 column 1 ID) the top (= highest) score. Then return the median of these
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53 top scores.
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54
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55 profile_type can be either "profile" or "avg_profile".
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56 "avg_profile means that the position-wise scores will first get smoothed
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57 out by calculating for each position a new score through taking a
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58 sequence window -avg_profile_extlr to +avg_profile_extlr of the position
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59 and calculate the mean score over this window and assign it to the
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60 position. After that, the maximum score of each site is chosen, and the
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61 median over all maximum scores is returned.
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62 "profile" leaves the position-wise scores as they are, directly extracting
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63 the maximum for each site and then reporting the median.
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64
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65 >>> test_file = "test-data/test.profile"
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66 >>> graphprot_profile_get_tsm(test_file)
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67 3.2
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adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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69 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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70 # Dictionary of lists, with list of scores (value) for each site (key).
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71 lists_dic = {}
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72 with open(profile_file) as f:
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73 for line in f:
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74 cols = line.strip().split("\t")
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75 seq_id = cols[0]
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76 score = float(cols[2])
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77 if seq_id in lists_dic:
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78 lists_dic[seq_id].append(score)
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79 else:
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80 lists_dic[seq_id] = []
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81 lists_dic[seq_id].append(score)
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82 f.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
83 # For each site, extract maximum and store in new list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
84 max_list = []
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
85 for seq_id in lists_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
86 if profile_type == "profile":
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
87 max_sc = max(lists_dic[seq_id])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
88 max_list.append(max_sc)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
89 elif profile_type == "avg_profile":
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
90 # Convert profile score list to average profile scores list.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
91 aps_list = \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
92 list_moving_window_average_values(lists_dic[seq_id],
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
93 win_extlr=avg_profile_extlr)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
94 max_sc = max(aps_list)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
95 max_list.append(max_sc)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
96 else:
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
97 assert 0, "invalid profile_type argument given: \"%s\"" \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
98 % (profile_type)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
99 # Return the median.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
100 return statistics.median(max_list)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
101
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
102
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
103 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
104
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
105 def list_moving_window_average_values(in_list,
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
106 win_extlr=5,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
107 method=1):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
108 """
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
109 Take a list of numeric values, and calculate for each position a new value,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
110 by taking the mean value of the window of positions -win_extlr and
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
111 +win_extlr. If full extension is not possible (at list ends), it just
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
112 takes what it gets.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
113 Two implementations of the task are given, chose by method=1 or method=2.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
114
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
115 >>> test_list = [2, 3, 5, 8, 4, 3, 7, 1]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
116 >>> list_moving_window_average_values(test_list, win_extlr=2, method=1)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
117 [3.3333333333333335, 4.5, 4.4, 4.6, 5.4, 4.6, 3.75, 3.6666666666666665]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
118 >>> list_moving_window_average_values(test_list, win_extlr=2, method=2)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
119 [3.3333333333333335, 4.5, 4.4, 4.6, 5.4, 4.6, 3.75, 3.6666666666666665]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
120
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
121 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
122 l_list = len(in_list)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
123 assert l_list, "Given list is empty"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
124 new_list = [0] * l_list
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
125 if win_extlr == 0:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
126 return l_list
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
127 if method == 1:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
128 for i in range(l_list):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
129 s = i - win_extlr
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
130 e = i + win_extlr + 1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
131 if s < 0:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
132 s = 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
133 if e > l_list:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
134 e = l_list
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
135 # Extract portion and assign value to new list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
136 new_list[i] = statistics.mean(in_list[s:e])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
137 elif method == 2:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
138 for i in range(l_list):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
139 s = i - win_extlr
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
140 e = i + win_extlr + 1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
141 if s < 0:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
142 s = 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
143 if e > l_list:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
144 e = l_list
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
145 ln = e - s
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
146 sc_sum = 0
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
147 for j in range(ln):
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
148 sc_sum += in_list[s + j]
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
149 new_list[i] = sc_sum / ln
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
150 else:
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
151 assert 0, "invalid method ID given (%i)" % (method)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
152 return new_list
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
153
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
154
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
155 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
156
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
157 def echo_add_to_file(echo_string, out_file):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
158 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
159 Add a string to file, using echo command.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
160
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
161 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
162 check_cmd = 'echo "%s" >> %s' % (echo_string, out_file)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
163 output = subprocess.getoutput(check_cmd)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
164 error = False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
165 if output:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
166 error = True
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
167 assert not error, "echo is complaining:\n%s\n%s" % (check_cmd, output)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
168
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
169
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
170 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
171
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
172 def is_tool(name):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
173 """Check whether tool "name" is in PATH."""
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
174 return find_executable(name) is not None
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
175
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
176
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
177 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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diff changeset
178
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
179 def count_fasta_headers(fasta_file):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
180 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
181 Count number of FASTA headers in fasta_file using grep.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
182
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
183 >>> test_file = "test-data/test.fa"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
184 >>> count_fasta_headers(test_file)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
185 2
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
186 >>> test_file = "test-data/empty_file"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
187 >>> count_fasta_headers(test_file)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
188 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
189
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
190 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
191 check_cmd = 'grep -c ">" ' + fasta_file
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
192 output = subprocess.getoutput(check_cmd)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
193 row_count = int(output.strip())
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
194 return row_count
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
195
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
196
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
197 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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diff changeset
198
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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diff changeset
199 def make_file_copy(in_file, out_file):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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diff changeset
200 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
201 Make a file copy by copying in_file to out_file.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
202
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
203 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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diff changeset
204 check_cmd = "cat " + in_file + " > " + out_file
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
205 assert in_file != out_file, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
206 "cat does not like to cat file into same file (%s)" % (check_cmd)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
207 output = subprocess.getoutput(check_cmd)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
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diff changeset
208 error = False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
209 if output:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
210 error = True
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
211 assert not error, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
212 "cat did not like your input (in_file: %s, out_file: %s):\n%s" \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
213 % (in_file, out_file, output)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
214
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
215
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
216 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
217
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
218 def split_fasta_into_test_train_files(in_fasta, test_out_fa, train_out_fa,
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
219 test_size=500):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
220 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
221 Split in_fasta .fa file into two files (e.g. test, train).
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
222
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
223 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
224 # Read in in_fasta.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
225 seqs_dic = read_fasta_into_dic(in_fasta)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
226 # Shuffle IDs.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
227 rand_ids_list = random_order_dic_keys_into_list(seqs_dic)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
228 c_out = 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
229 TESTOUT = open(test_out_fa, "w")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
230 TRAINOUT = open(train_out_fa, "w")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
231 for seq_id in rand_ids_list:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
232 seq = seqs_dic[seq_id]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
233 if (c_out >= test_size):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
234 TRAINOUT.write(">%s\n%s\n" % (seq_id, seq))
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
235 else:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
236 TESTOUT.write(">%s\n%s\n" % (seq_id, seq))
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
237 c_out += 1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
238 TESTOUT.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
239 TRAINOUT.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
240
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
241
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
242 ###############################################################################
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
243
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
244 def check_seqs_dic_format(seqs_dic):
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
245 """
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
246 Check sequence dictionary for lowercase-only sequences or sequences
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
247 wich have lowercase nts in between uppercase nts.
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
248 Return suspicious IDs as list or empty list if not hits.
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
249 IDs with lowercase-only sequences.
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
250
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
251 >>> seqs_dic = {"id1" : "acguACGU", "id2" : "acgua", "id3" : "acgUUaUcc"}
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
252 >>> check_seqs_dic_format(seqs_dic)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
253 ['id2', 'id3']
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
254 >>> seqs_dic = {"id1" : "acgAUaa", "id2" : "ACGUACUA"}
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
255 >>> check_seqs_dic_format(seqs_dic)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
256 []
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
257
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
258 """
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
259 assert seqs_dic, "given seqs_dic empty"
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
260 bad_seq_ids = []
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
261 for seq_id in seqs_dic:
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
262 seq = seqs_dic[seq_id]
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
263 if re.search("^[acgtun]+$", seq):
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
264 bad_seq_ids.append(seq_id)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
265 if re.search("[ACGTUN][acgtun]+[ACGTUN]", seq):
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
266 bad_seq_ids.append(seq_id)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
267 return bad_seq_ids
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
268
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
269
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
270 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
271
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
272 def read_fasta_into_dic(fasta_file,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
273 seqs_dic=False,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
274 ids_dic=False,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
275 read_dna=False,
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
276 short_ensembl=False,
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
277 reject_lc=False,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
278 convert_to_uc=False,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
279 skip_n_seqs=True):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
280 """
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
281 Read in FASTA sequences, convert to RNA, store in dictionary
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
282 and return dictionary.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
283
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
284 >>> test_fasta = "test-data/test.fa"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
285 >>> read_fasta_into_dic(test_fasta)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
286 {'seq1': 'acguACGUacgu', 'seq2': 'ugcaUGCAugcaACGUacgu'}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
287 >>> test_fasta = "test-data/test2.fa"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
288 >>> read_fasta_into_dic(test_fasta)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
289 {}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
290 >>> test_fasta = "test-data/test.ensembl.fa"
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
291 >>> read_fasta_into_dic(test_fasta, read_dna=True, short_ensembl=True)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
292 {'ENST00000415118': 'GAAATAGT', 'ENST00000448914': 'ACTGGGGGATACGAAAA'}
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
293 >>> test_fasta = "test-data/test4.fa"
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
294 >>> read_fasta_into_dic(test_fasta)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
295 {'1': 'gccuAUGUuuua', '2': 'cugaAACUaugu'}
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
296
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
297 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
298 if not seqs_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
299 seqs_dic = {}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
300 seq_id = ""
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
301 seq = ""
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
302
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
303 # Go through FASTA file, extract sequences.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
304 if re.search(r".+\.gz$", fasta_file):
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
305 f = gzip.open(fasta_file, 'rt')
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
306 else:
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
307 f = open(fasta_file, "r")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
308 for line in f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
309 if re.search(">.+", line):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
310 m = re.search(">(.+)", line)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
311 seq_id = m.group(1)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
312 # If there is a ".", take only first part of header.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
313 # This assumes ENSEMBL header format ">ENST00000631435.1 cdna ..."
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
314 if short_ensembl:
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
315 if re.search(r".+\..+", seq_id):
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
316 m = re.search(r"(.+?)\..+", seq_id)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
317 seq_id = m.group(1)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
318 assert seq_id not in seqs_dic, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
319 "non-unique FASTA header \"%s\" in \"%s\"" \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
320 % (seq_id, fasta_file)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
321 if ids_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
322 if seq_id in ids_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
323 seqs_dic[seq_id] = ""
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
324 else:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
325 seqs_dic[seq_id] = ""
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
326 elif re.search("[ACGTUN]+", line, re.I):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
327 if seq_id in seqs_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
328 m = re.search("([ACGTUN]+)", line, re.I)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
329 seq = m.group(1)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
330 if reject_lc:
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
331 assert \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
332 not re.search("[a-z]", seq), \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
333 "lc char detected in seq \"%i\" (reject_lc=True)" \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
334 % (seq_id)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
335 if convert_to_uc:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
336 seq = seq.upper()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
337 # If sequences with N nucleotides should be skipped.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
338 if skip_n_seqs:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
339 if "n" in m.group(1) or "N" in m.group(1):
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
340 print("WARNING: \"%s\" contains N. Discarding "
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
341 "sequence ... " % (seq_id))
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
342 del seqs_dic[seq_id]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
343 continue
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
344 # Convert to RNA, concatenate sequence.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
345 if read_dna:
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
346 seqs_dic[seq_id] += \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
347 m.group(1).replace("U", "T").replace("u", "t")
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
348 else:
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
349 seqs_dic[seq_id] += \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
350 m.group(1).replace("T", "U").replace("t", "u")
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
351 f.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
352 return seqs_dic
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
353
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
354
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
355 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
356
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
357 def random_order_dic_keys_into_list(in_dic):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
358 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
359 Read in dictionary keys, and return random order list of IDs.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
360
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
361 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
362 id_list = []
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
363 for key in in_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
364 id_list.append(key)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
365 random.shuffle(id_list)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
366 return id_list
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
367
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
368
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
369 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
370
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
371 def graphprot_get_param_string(params_file):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
372 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
373 Get parameter string from GraphProt .params file.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
374
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
375 >>> test_params = "test-data/test.params"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
376 >>> graphprot_get_param_string(test_params)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
377 '-epochs 20 -lambda 0.01 -R 1 -D 3 -bitsize 14 -onlyseq '
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
378
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
379 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
380 param_string = ""
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
381 with open(params_file) as f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
382 for line in f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
383 cols = line.strip().split(" ")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
384 param = cols[0]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
385 setting = cols[1]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
386 if re.search(".+:", param):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
387 m = re.search("(.+):", line)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
388 par = m.group(1)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
389 if re.search("pos_train.+", line):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
390 continue
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
391 if par == "model_type":
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
392 if setting == "sequence":
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
393 param_string += "-onlyseq "
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
394 else:
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
395 param_string += "-%s %s " % (par, setting)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
396 else:
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
397 assert 0, "pattern matching failed for string \"%s\"" % (param)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
398 return param_string
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
399
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
400
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
401 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
402
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
403 def seqs_dic_count_uc_nts(seqs_dic):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
404 """
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
405 Count number of uppercase nucleotides in sequences stored in sequence
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
406 dictionary.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
407
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
408 >>> seqs_dic = {'seq1': "acgtACGTacgt", 'seq2': 'acgtACacgt'}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
409 >>> seqs_dic_count_uc_nts(seqs_dic)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
410 6
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
411 >>> seqs_dic = {'seq1': "acgtacgt", 'seq2': 'acgtacgt'}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
412 >>> seqs_dic_count_uc_nts(seqs_dic)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
413 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
414
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
415 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
416 assert seqs_dic, "Given sequence dictionary empty"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
417 c_uc = 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
418 for seq_id in seqs_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
419 c_uc += len(re.findall(r'[A-Z]', seqs_dic[seq_id]))
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
420 return c_uc
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
421
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
422
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
423 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
424
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
425 def seqs_dic_count_lc_nts(seqs_dic):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
426 """
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
427 Count number of lowercase nucleotides in sequences stored in sequence
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
428 dictionary.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
429
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
430 >>> seqs_dic = {'seq1': "gtACGTac", 'seq2': 'cgtACacg'}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
431 >>> seqs_dic_count_lc_nts(seqs_dic)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
432 10
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
433 >>> seqs_dic = {'seq1': "ACGT", 'seq2': 'ACGTAC'}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
434 >>> seqs_dic_count_lc_nts(seqs_dic)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
435 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
436
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
437 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
438 assert seqs_dic, "Given sequence dictionary empty"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
439 c_uc = 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
440 for seq_id in seqs_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
441 c_uc += len(re.findall(r'[a-z]', seqs_dic[seq_id]))
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
442 return c_uc
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
443
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
444
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
445 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
446
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
447 def count_file_rows(in_file):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
448 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
449 Count number of file rows for given input file.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
450
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
451 >>> test_file = "test-data/test1.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
452 >>> count_file_rows(test_file)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
453 7
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
454 >>> test_file = "test-data/empty_file"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
455 >>> count_file_rows(test_file)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
456 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
457
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
458 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
459 check_cmd = "cat " + in_file + " | wc -l"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
460 output = subprocess.getoutput(check_cmd)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
461 row_count = int(output.strip())
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
462 return row_count
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
463
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
464
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
465 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
466
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
467 def bed_check_six_col_format(bed_file):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
468 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
469 Check whether given .bed file has 6 columns.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
470
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
471 >>> test_bed = "test-data/test1.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
472 >>> bed_check_six_col_format(test_bed)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
473 True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
474 >>> test_bed = "test-data/empty_file"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
475 >>> bed_check_six_col_format(test_bed)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
476 False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
477
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
478 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
479
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
480 six_col_format = False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
481 with open(bed_file) as f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
482 for line in f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
483 cols = line.strip().split("\t")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
484 if len(cols) == 6:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
485 six_col_format = True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
486 break
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
487 f.closed
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
488 return six_col_format
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
489
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
490
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
491 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
492
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
493 def bed_check_unique_ids(bed_file):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
494 """
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
495 Check whether .bed file (6 column format with IDs in column 4)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
496 has unique column 4 IDs.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
497
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
498 >>> test_bed = "test-data/test1.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
499 >>> bed_check_unique_ids(test_bed)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
500 True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
501 >>> test_bed = "test-data/test2.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
502 >>> bed_check_unique_ids(test_bed)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
503 False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
504
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
505 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
506
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
507 check_cmd = "cut -f 4 " + bed_file + " | sort | uniq -d"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
508 output = subprocess.getoutput(check_cmd)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
509 if output:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
510 return False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
511 else:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
512 return True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
513
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
514
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
515 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
516
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
517 def get_seq_lengths_from_seqs_dic(seqs_dic):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
518 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
519 Given a dictionary of sequences, return dictionary of sequence lengths.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
520 Mapping is sequence ID -> sequence length.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
521 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
522 seq_len_dic = {}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
523 assert seqs_dic, "sequence dictionary seems to be empty"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
524 for seq_id in seqs_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
525 seq_l = len(seqs_dic[seq_id])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
526 seq_len_dic[seq_id] = seq_l
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
527 return seq_len_dic
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
528
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
529
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
530 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
531
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
532 def bed_get_region_lengths(bed_file):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
533 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
534 Read in .bed file, store and return region lengths in dictionary.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
535 key : region ID (.bed col4)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
536 value : region length (.bed col3-col2)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
537
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
538 >>> test_file = "test-data/test4.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
539 >>> bed_get_region_lengths(test_file)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
540 {'CLIP1': 10, 'CLIP2': 10}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
541
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
542 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
543 id2len_dic = {}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
544 with open(bed_file) as f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
545 for line in f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
546 cols = line.strip().split("\t")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
547 site_s = int(cols[1])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
548 site_e = int(cols[2])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
549 site_id = cols[3]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
550 site_l = site_e - site_s
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
551 assert site_id \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
552 not in id2len_dic, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
553 "column 4 IDs not unique in given .bed file \"%s\"" \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
554 % (bed_file)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
555 id2len_dic[site_id] = site_l
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
556 f.closed
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
557 assert id2len_dic, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
558 "No IDs read into dic (input file \"%s\" empty or malformatted?)" \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
559 % (bed_file)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
560 return id2len_dic
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
561
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
562
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
563 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
564
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
565 def graphprot_get_param_dic(params_file):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
566 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
567 Read in GraphProt .params file and store in dictionary.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
568 key = parameter
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
569 value = parameter value
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
570
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
571 >>> params_file = "test-data/test.params"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
572 >>> graphprot_get_param_dic(params_file)
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
573 {'epochs': '20', 'lambda': '0.01', 'R': '1', 'D': '3', 'bitsize': '14', \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
574 'model_type': 'sequence', 'pos_train_ws_pred_median': '0.760321', \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
575 'pos_train_profile_median': '5.039610', \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
576 'pos_train_avg_profile_median_1': '4.236340', \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
577 'pos_train_avg_profile_median_2': '3.868431', \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
578 'pos_train_avg_profile_median_3': '3.331277', \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
579 'pos_train_avg_profile_median_4': '2.998667', \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
580 'pos_train_avg_profile_median_5': '2.829782', \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
581 'pos_train_avg_profile_median_6': '2.626623', \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
582 'pos_train_avg_profile_median_7': '2.447083', \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
583 'pos_train_avg_profile_median_8': '2.349919', \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
584 'pos_train_avg_profile_median_9': '2.239829', \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
585 'pos_train_avg_profile_median_10': '2.161676'}
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
586
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
587 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
588 param_dic = {}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
589 with open(params_file) as f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
590 for line in f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
591 cols = line.strip().split(" ")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
592 param = cols[0]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
593 setting = cols[1]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
594 if re.search(".+:", param):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
595 m = re.search("(.+):", line)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
596 par = m.group(1)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
597 param_dic[par] = setting
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
598 f.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
599 return param_dic
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
600
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
601
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
602 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
603
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
604 def graphprot_filter_predictions_file(in_file, out_file,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
605 sc_thr=0):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
606 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
607 Filter GraphProt .predictions file by given score thr_sc.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
608 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
609 OUTPRED = open(out_file, "w")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
610 with open(in_file) as f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
611 for line in f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
612 row = line.strip()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
613 cols = line.strip().split("\t")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
614 score = float(cols[2])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
615 if score < sc_thr:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
616 continue
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
617 OUTPRED.write("%s\n" % (row))
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
618 f.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
619 OUTPRED.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
620
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
621
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
622 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
623
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
624 def fasta_read_in_ids(fasta_file):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
625 """
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
626 Given a .fa file, read in header IDs in order appearing in file,
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
627 and store in list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
628
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
629 >>> test_file = "test-data/test3.fa"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
630 >>> fasta_read_in_ids(test_file)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
631 ['SERBP1_K562_rep01_544', 'SERBP1_K562_rep02_709', 'SERBP1_K562_rep01_316']
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
632
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
633 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
634 ids_list = []
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
635 with open(fasta_file) as f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
636 for line in f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
637 if re.search(">.+", line):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
638 m = re.search(">(.+)", line)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
639 seq_id = m.group(1)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
640 ids_list.append(seq_id)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
641 f.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
642 return ids_list
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
643
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
644
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
645 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
646
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
647 def graphprot_profile_calc_avg_profile(in_file, out_file,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
648 ap_extlr=5,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
649 seq_ids_list=False,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
650 method=1):
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
651 """
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
652 Given a GraphProt .profile file, calculate average profiles and output
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
653 average profile file.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
654 Average profile means that the position-wise scores will get smoothed
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
655 out by calculating for each position a new score, taking a sequence
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
656 window -ap_extlr to +ap_extlr relative to the position
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
657 and calculate the mean score over this window. The mean score then
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
658 becomes the new average profile score at this position.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
659 Two different implementations of the task are given:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
660 method=1 (new python implementation, slower + more memory but easy to read)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
661 method=2 (old perl implementation, faster and less memory but more code)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
662
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
663 >>> in_file = "test-data/test2.profile"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
664 >>> out_file1 = "test-data/test2_1.avg_profile"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
665 >>> out_file2 = "test-data/test2_2.avg_profile"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
666 >>> out_file4 = "test-data/test2_3.avg_profile"
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
667 >>> graphprot_profile_calc_avg_profile(in_file, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
668 out_file1, ap_extlr=2, method=1)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
669 >>> graphprot_profile_calc_avg_profile(in_file, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
670 out_file2, ap_extlr=2, method=2)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
671 >>> diff_two_files_identical(out_file1, out_file2)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
672 True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
673 >>> test_list = ["s1", "s2", "s3", "s4"]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
674 >>> out_file3_exp = "test-data/test3_added_ids_exp.avg_profile"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
675 >>> out_file3 = "test-data/test3_added_ids_out.avg_profile"
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
676 >>> graphprot_profile_calc_avg_profile(in_file, out_file3, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
677 ap_extlr=2, method=1, seq_ids_list=test_list)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
678 >>> diff_two_files_identical(out_file3_exp, out_file3)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
679 True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
680
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
681 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
682 if method == 1:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
683 # Dictionary of lists, with list of scores (value) for each site (key).
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
684 lists_dic = {}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
685 site_starts_dic = {}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
686 with open(in_file) as f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
687 for line in f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
688 cols = line.strip().split("\t")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
689 site_id = int(cols[0])
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
690 pos = int(cols[1]) # 0-based.
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
691 score = float(cols[2])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
692 # Store first position of site.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
693 if site_id not in site_starts_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
694 site_starts_dic[site_id] = pos
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
695 if site_id in lists_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
696 lists_dic[site_id].append(score)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
697 else:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
698 lists_dic[site_id] = []
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
699 lists_dic[site_id].append(score)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
700 f.close()
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
701 # Check number of IDs (# FASTA IDs has to be same as # site IDs).
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
702 if seq_ids_list:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
703 c_seq_ids = len(seq_ids_list)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
704 c_site_ids = len(site_starts_dic)
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
705 assert c_seq_ids == c_site_ids, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
706 "# sequence IDs != # site IDs (%i != %i)" \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
707 % (c_seq_ids, c_site_ids)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
708 OUTPROF = open(out_file, "w")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
709 # For each site, calculate average profile scores list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
710 for site_id in lists_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
711 # Convert profile score list to average profile scores list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
712 aps_list = list_moving_window_average_values(lists_dic[site_id],
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
713 win_extlr=ap_extlr)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
714 start_pos = site_starts_dic[site_id]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
715 # Get original FASTA sequence ID.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
716 if seq_ids_list:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
717 site_id = seq_ids_list[site_id]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
718 for i, sc in enumerate(aps_list):
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
719 pos = i + start_pos + 1 # make 1-based.
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
720 OUTPROF.write("%s\t%i\t%f\n" % (site_id, pos, sc))
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
721 OUTPROF.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
722 elif method == 2:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
723 OUTPROF = open(out_file, "w")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
724 # Old site ID.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
725 old_id = ""
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
726 # Current site ID.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
727 cur_id = ""
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
728 # Scores list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
729 scores_list = []
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
730 site_starts_dic = {}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
731 with open(in_file) as f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
732 for line in f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
733 cols = line.strip().split("\t")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
734 cur_id = int(cols[0])
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
735 pos = int(cols[1]) # 0-based.
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
736 score = float(cols[2])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
737 # Store first position of site.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
738 if cur_id not in site_starts_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
739 site_starts_dic[cur_id] = pos
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
740 # Case: new site (new column 1 ID).
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
741 if cur_id != old_id:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
742 # Process old id scores.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
743 if scores_list:
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
744 aps_list = \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
745 list_moving_window_average_values(
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
746 scores_list,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
747 win_extlr=ap_extlr)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
748 start_pos = site_starts_dic[old_id]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
749 seq_id = old_id
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
750 # Get original FASTA sequence ID.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
751 if seq_ids_list:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
752 seq_id = seq_ids_list[old_id]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
753 for i, sc in enumerate(aps_list):
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
754 pos = i + start_pos + 1 # make 1-based.
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
755 OUTPROF.write("%s\t%i\t%f\n" % (seq_id, pos, sc))
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
756 # Reset list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
757 scores_list = []
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
758 old_id = cur_id
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
759 scores_list.append(score)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
760 else:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
761 # Add to scores_list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
762 scores_list.append(score)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
763 f.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
764 # Process last block.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
765 if scores_list:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
766 aps_list = list_moving_window_average_values(scores_list,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
767 win_extlr=ap_extlr)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
768 start_pos = site_starts_dic[old_id]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
769 seq_id = old_id
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
770 # Get original FASTA sequence ID.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
771 if seq_ids_list:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
772 seq_id = seq_ids_list[old_id]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
773 for i, sc in enumerate(aps_list):
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
774 pos = i + start_pos + 1 # make 1-based.
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
775 OUTPROF.write("%s\t%i\t%f\n" % (seq_id, pos, sc))
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
776 OUTPROF.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
777
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
778
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
779 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
780
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
781 def graphprot_profile_extract_peak_regions(in_file, out_file,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
782 max_merge_dist=0,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
783 sc_thr=0):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
784 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
785 Extract peak regions from GraphProt .profile file.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
786 Store the peak regions (defined as regions with scores >= sc_thr)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
787 as to out_file in 6-column .bed.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
788
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
789 TODO:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
790 Add option for genomic coordinates input (+ - polarity support).
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
791 Output genomic regions instead of sequence regions.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
792
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
793 >>> in_file = "test-data/test4.avg_profile"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
794 >>> out_file = "test-data/test4_out.peaks.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
795 >>> exp_file = "test-data/test4_out_exp.peaks.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
796 >>> exp2_file = "test-data/test4_out_exp2.peaks.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
797 >>> empty_file = "test-data/empty_file"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
798 >>> graphprot_profile_extract_peak_regions(in_file, out_file)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
799 >>> diff_two_files_identical(out_file, exp_file)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
800 True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
801 >>> graphprot_profile_extract_peak_regions(in_file, out_file, sc_thr=10)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
802 >>> diff_two_files_identical(out_file, empty_file)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
803 True
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
804 >>> graphprot_profile_extract_peak_regions(in_file, out_file, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
805 max_merge_dist=2)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
806 >>> diff_two_files_identical(out_file, exp2_file)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
807 True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
808
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
809 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
810
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
811 OUTPEAKS = open(out_file, "w")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
812 # Old site ID.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
813 old_id = ""
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
814 # Current site ID.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
815 cur_id = ""
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
816 # Scores list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
817 scores_list = []
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
818 site_starts_dic = {}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
819 with open(in_file) as f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
820 for line in f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
821 cols = line.strip().split("\t")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
822 cur_id = cols[0]
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
823 pos = int(cols[1]) # 0-based.
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
824 score = float(cols[2])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
825 # Store first position of site.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
826 if cur_id not in site_starts_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
827 # If first position != zero, we assume positions are 1-based.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
828 if pos != 0:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
829 # Make index 0-based.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
830 site_starts_dic[cur_id] = pos - 1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
831 else:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
832 site_starts_dic[cur_id] = pos
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
833 # Case: new site (new column 1 ID).
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
834 if cur_id != old_id:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
835 # Process old id scores.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
836 if scores_list:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
837 # Extract peaks from region.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
838 peak_list = \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
839 list_extract_peaks(scores_list,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
840 max_merge_dist=max_merge_dist,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
841 coords="bed",
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
842 sc_thr=sc_thr)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
843 start_pos = site_starts_dic[old_id]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
844 # Print out peaks in .bed format.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
845 for ln in peak_list:
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
846 peak_s = start_pos + ln[0]
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
847 peak_e = start_pos + ln[1]
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
848 site_id = "%s,%i" % (old_id, ln[2])
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
849 OUTPEAKS.write("%s\t%i\t%i"
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
850 "\t%s\t%f\t+\n"
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
851 % (old_id, peak_s,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
852 peak_e, site_id, ln[3]))
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
853 # Reset list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
854 scores_list = []
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
855 old_id = cur_id
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
856 scores_list.append(score)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
857 else:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
858 # Add to scores_list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
859 scores_list.append(score)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
860 f.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
861 # Process last block.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
862 if scores_list:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
863 # Extract peaks from region.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
864 peak_list = list_extract_peaks(scores_list,
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
865 max_merge_dist=max_merge_dist,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
866 coords="bed",
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
867 sc_thr=sc_thr)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
868 start_pos = site_starts_dic[old_id]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
869 # Print out peaks in .bed format.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
870 for ln in peak_list:
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
871 peak_s = start_pos + ln[0]
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
872 peak_e = start_pos + ln[1]
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
873 site_id = "%s,%i" % (old_id, ln[2]) # best score also 1-based.
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
874 OUTPEAKS.write("%s\t%i\t%i\t%s\t%f\t+\n"
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
875 % (old_id, peak_s, peak_e, site_id, ln[3]))
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
876 OUTPEAKS.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
877
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
878
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
879 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
880
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
881 def list_extract_peaks(in_list,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
882 max_merge_dist=0,
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
883 coords="list",
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
884 sc_thr=0):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
885 """
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
886 Extract peak regions from list.
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
887 Peak region is defined as region >= score threshold.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
888
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
889 coords=bed : peak start 0-based, peak end 1-based.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
890 coords=list : peak start 0-based, peak end 0-based.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
891
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
892 >>> test_list = [-1, 0, 2, 4.5, 1, -1, 5, 6.5]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
893 >>> list_extract_peaks(test_list)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
894 [[1, 4, 3, 4.5], [6, 7, 7, 6.5]]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
895 >>> list_extract_peaks(test_list, sc_thr=2)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
896 [[2, 3, 3, 4.5], [6, 7, 7, 6.5]]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
897 >>> list_extract_peaks(test_list, sc_thr=2, coords="bed")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
898 [[2, 4, 4, 4.5], [6, 8, 8, 6.5]]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
899 >>> list_extract_peaks(test_list, sc_thr=10)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
900 []
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
901 >>> test_list = [2, -1, 3, -1, 4, -1, -1, 6, 9]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
902 >>> list_extract_peaks(test_list, max_merge_dist=2)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
903 [[0, 4, 4, 4], [7, 8, 8, 9]]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
904 >>> list_extract_peaks(test_list, max_merge_dist=3)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
905 [[0, 8, 8, 9]]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
906
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
907 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
908 # Check.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
909 assert len(in_list), "Given list is empty"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
910 # Peak regions list.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
911 peak_list = []
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
912 # Help me.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
913 inside = False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
914 pr_s = 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
915 pr_e = 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
916 pr_top_pos = 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
917 pr_top_sc = -100000
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
918 for i, sc in enumerate(in_list):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
919 # Part of peak region?
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
920 if sc >= sc_thr:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
921 # At peak start.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
922 if not inside:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
923 pr_s = i
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
924 pr_e = i
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
925 inside = True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
926 else:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
927 # Inside peak region.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
928 pr_e = i
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
929 # Store top position.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
930 if sc > pr_top_sc:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
931 pr_top_sc = sc
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
932 pr_top_pos = i
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
933 else:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
934 # Before was peak region?
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
935 if inside:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
936 # Store peak region.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
937 peak_infos = [pr_s, pr_e, pr_top_pos, pr_top_sc]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
938 peak_list.append(peak_infos)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
939 inside = False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
940 pr_top_pos = 0
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
941 pr_top_sc = -100000
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
942 # If peak at the end, also report.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
943 if inside:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
944 # Store peak region.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
945 peak_infos = [pr_s, pr_e, pr_top_pos, pr_top_sc]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
946 peak_list.append(peak_infos)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
947 # Merge peaks.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
948 if max_merge_dist and len(peak_list) > 1:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
949 iterate = True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
950 while iterate:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
951 merged_peak_list = []
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
952 added_peaks_dic = {}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
953 peaks_merged = False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
954 for i, l in enumerate(peak_list):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
955 if i in added_peaks_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
956 continue
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
957 j = i + 1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
958 # Last element.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
959 if j == len(peak_list):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
960 if i not in added_peaks_dic:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
961 merged_peak_list.append(peak_list[i])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
962 break
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
963 # Compare two elements.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
964 new_peak = []
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
965 if (peak_list[j][0] - peak_list[i][1]) <= max_merge_dist:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
966 peaks_merged = True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
967 new_top_pos = peak_list[i][2]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
968 new_top_sc = peak_list[i][3]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
969 if peak_list[i][3] < peak_list[j][3]:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
970 new_top_pos = peak_list[j][2]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
971 new_top_sc = peak_list[j][3]
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
972 new_peak = [peak_list[i][0], peak_list[j][1],
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
973 new_top_pos, new_top_sc]
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
974 # If two peaks were merged.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
975 if new_peak:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
976 merged_peak_list.append(new_peak)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
977 added_peaks_dic[i] = 1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
978 added_peaks_dic[j] = 1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
979 else:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
980 merged_peak_list.append(peak_list[i])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
981 added_peaks_dic[i] = 1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
982 if not peaks_merged:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
983 iterate = False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
984 peak_list = merged_peak_list
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
985 peaks_merged = False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
986 # If peak coordinates should be in .bed format, make peak ends 1-based.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
987 if coords == "bed":
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
988 for i in range(len(peak_list)):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
989 peak_list[i][1] += 1
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
990 peak_list[i][2] += 1 # 1-base best score position too.
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
991 return peak_list
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
992
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
993
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
994 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
995
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
996 def bed_peaks_to_genomic_peaks(peak_file, genomic_peak_file, genomic_sites_bed,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
997 print_rows=False):
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
998 """
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
999 Given a .bed file of sequence peak regions (possible coordinates from
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1000 0 to length of s), convert peak coordinates to genomic coordinates.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1001 Do this by taking genomic regions of sequences as input.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1002
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1003 >>> test_in = "test-data/test.peaks.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1004 >>> test_exp = "test-data/test_exp.peaks.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1005 >>> test_out = "test-data/test_out.peaks.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1006 >>> gen_in = "test-data/test.peaks_genomic.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1007 >>> bed_peaks_to_genomic_peaks(test_in, test_out, gen_in)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1008 >>> diff_two_files_identical(test_out, test_exp)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1009 True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1010
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1011 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1012 # Read in genomic region info.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1013 id2row_dic = {}
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1014
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1015 with open(genomic_sites_bed) as f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1016 for line in f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1017 row = line.strip()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1018 cols = line.strip().split("\t")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1019 site_id = cols[3]
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1020 assert site_id \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1021 not in id2row_dic, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1022 "column 4 IDs not unique in given .bed file \"%s\"" \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1023 % (genomic_sites_bed)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1024 id2row_dic[site_id] = row
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1025 f.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1026
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1027 # Read in peaks file and convert coordinates.
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1028 OUTPEAKS = open(genomic_peak_file, "w")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1029 with open(peak_file) as f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1030 for line in f:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1031 cols = line.strip().split("\t")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1032 site_id = cols[0]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1033 site_s = int(cols[1])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1034 site_e = int(cols[2])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1035 site_id2 = cols[3]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1036 site_sc = float(cols[4])
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1037 assert re.search(".+,.+", site_id2), \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1038 "regular expression failed for ID \"%s\"" % (site_id2)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1039 m = re.search(r".+,(\d+)", site_id2)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1040 sc_pos = int(m.group(1)) # 1-based.
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1041 assert site_id in id2row_dic, \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1042 "site ID \"%s\" not found in genomic sites dictionary" \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1043 % (site_id)
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1044 row = id2row_dic[site_id]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1045 rowl = row.split("\t")
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1046 gen_chr = rowl[0]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1047 gen_s = int(rowl[1])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1048 gen_e = int(rowl[2])
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1049 gen_pol = rowl[5]
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1050 new_s = site_s + gen_s
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1051 new_e = site_e + gen_s
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1052 new_sc_pos = sc_pos + gen_s
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1053 if gen_pol == "-":
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1054 new_s = gen_e - site_e
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1055 new_e = gen_e - site_s
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1056 new_sc_pos = gen_e - sc_pos + 1 # keep 1-based.
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1057 new_row = "%s\t%i\t%i\t%s,%i\t%f\t%s" \
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1058 % (gen_chr, new_s, new_e,
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1059 site_id, new_sc_pos, site_sc, gen_pol)
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1060 OUTPEAKS.write("%s\n" % (new_row))
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1061 if print_rows:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1062 print(new_row)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1063 OUTPEAKS.close()
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1064
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1065
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1066 ###############################################################################
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1067
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1068 def diff_two_files_identical(file1, file2):
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1069 """
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1070 Check whether two files are identical. Return true if diff reports no
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1071 differences.
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1072
1
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1073 >>> file1 = "test-data/file1"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1074 >>> file2 = "test-data/file2"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1075 >>> diff_two_files_identical(file1, file2)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1076 True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1077 >>> file1 = "test-data/test1.bed"
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1078 >>> diff_two_files_identical(file1, file2)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1079 False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1080
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1081 """
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1082 same = True
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1083 check_cmd = "diff " + file1 + " " + file2
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1084 output = subprocess.getoutput(check_cmd)
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1085 if output:
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1086 same = False
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1087 return same
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1088
adcc4c457c3c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
1089
3
9a83a84a25a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
1090 ###############################################################################