Mercurial > repos > abims-sbr > pairwise

annotate scripts/S09_post_processing_of_pairwise.py @ 1:c8af52875b0f draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
author lecorguille
date Thu, 13 Apr 2017 09:46:45 -0400
parents
children 6709645eff5d
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c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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1 #!/usr/bin/env python
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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2 ## AUTHOR: Eric Fontanillas
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3 ## LAST VERSION: 14/08/14 by Julie BAFFARD
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5 MINIMUM_LENGTH = 1
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7 ############################
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8 ##### DEF1 : Get Pairs #####
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9 ############################
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10 def get_pairs(fasta_file_path):
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11 F2 = open(fasta_file_path, "r")
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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12 list_pairwises = []
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13 while 1:
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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14 next2 = F2.readline()
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15 if not next2:
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16 break
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17 if next2[0] == ">":
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18 fasta_name_query = next2[:-1]
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19 next3 = F2.readline()
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20 fasta_seq_query = next3[:-1]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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21 next3 = F2.readline() ## jump one empty line (if any after the sequence)
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22 fasta_name_match = next3[:-1]
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23 next3 = F2.readline()
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24 fasta_seq_match = next3[:-1]
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25 pairwise = [fasta_name_query,fasta_seq_query,fasta_name_match,fasta_seq_match]
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27 ## ADD pairwise with condition
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28 list_pairwises.append(pairwise)
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29 F2.close()
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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30 return(list_pairwises)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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31 ##############################################
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34 #################################
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35 ##### DEF2 : Extract length #####
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36 #################################
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37 def extract_length(length_string): # format length string = 57...902
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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38 l3 = string.split(length_string, "...")
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39 n1 = string.atoi(l3[0])
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40 n2 = string.atoi(l3[1])
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41 length = n2-n1
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42 return(length)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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43 ##############################################
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46 ####################################
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47 ##### DEF3 : Remove Redondancy #####
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48 ####################################
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49 def filter_redondancy(list_paireu, MIN_LENGTH):
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51 bash1 = {}
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52 list_pairout = []
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54 for pair in list_paireu:
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55 query_name = pair[0]
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56 query_seq = pair[1]
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57 match_name = pair[2]
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58 match_seq = pair[3]
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59
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60 l1 = string.split(query_name, "||")
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61 short_query_name = l1[0][1:]
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62 length_matched = extract_length(l1[1]) ### DEF2 ###
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63 l2 = string.split(match_name, "||")
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64 short_match_name = l2[0][1:]
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65 binom = "%s_%s" %(short_query_name, short_match_name)
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66
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67 if binom not in bash1.keys():
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68 bash1[binom] = [query_name, query_seq, match_name, match_seq, length_matched]
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69 else:
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70 old_length = bash1[binom][-1]
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71 if length_matched > old_length:
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72 bash1[binom] = [query_name, query_seq, match_name, match_seq, length_matched]
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73
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75 for bino in bash1.keys():
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76 length = bash1[bino][-1]
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77 if length > MIN_LENGTH:
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78 list_pairout.append(bash1[bino])
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81 return(list_pairout)
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82 ##############################################
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84
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85 #######################
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86 ##### RUN RUN RUN #####
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87 #######################
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88 import string, os, time, re, sys
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89
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90 ## 1 ## INPUT/OUTPUT
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91 SHORT_FILE = sys.argv[1] ## short-name-query_short-name-db
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92
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93 F_IN = "%s/13_PairwiseMatch_%s.fasta" %(SHORT_FILE, SHORT_FILE)
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94
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95 F_OUT = "%s/15_PairwiseMatch_filtered_%s.fasta" %(SHORT_FILE, SHORT_FILE)
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96 File_OUT = open(F_OUT, "w")
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97
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98 ## 2 ## RUN
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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99 list_pairwises = get_pairs(F_IN) ### DEF1 ###
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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100
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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101 list_pairwises_filtered1 = filter_redondancy(list_pairwises, MINIMUM_LENGTH) ### DEF3 ###
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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102
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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103
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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104 i = 0
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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105 for pair in list_pairwises_filtered1:
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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106 i = i+1
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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107
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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108 ## Write pairwise alignment
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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109 File_OUT.write("%s\n" %pair[0])
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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110 File_OUT.write("%s\n" %pair[1])
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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111 File_OUT.write("%s\n" %pair[2])
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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112 File_OUT.write("%s\n" %pair[3])
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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113
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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114 File_OUT.close()