Mercurial > repos > abims-sbr > pairwise

annotate scripts/S08_script_extract_match_v20_blastx.py @ 8:471ed956ff13 draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit b7a3030ea134b5dfad89b1a869db659d72d1145c
author abims-sbr
date Wed, 28 Feb 2018 10:37:14 -0500
parents 6709645eff5d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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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c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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5 ### TBLASTX formatting
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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7 ### MATCH = Only the first match keeped
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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8 MATCH = 0 # Only 1rst match Wanted
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6709645eff5d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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9 #MATCH = 1 # All match wanted
6709645eff5d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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1
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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11 ### SUBMATCH = several part of a same sequence match with the query
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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12 SUBMATCH = 0 # SUBMATCH NOT WANTED (ONLY 1rst HIT)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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13 #SUBMATCH =1 # SUBMATCH WANTED
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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16 ### NAME FORMATTING:
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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17 # [A] FORMAT QUERY NAME 1st STEP [IN DEF1]
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19 # [B] FORMAT MATCH NAME 1st STEP [IN DEF2.1]
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21 # [C] FORMAT MATCH NAME 2nd STEP [MIDDLE of DEF 2.3]
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22 # [D] FORMAT QUERY NAME 2nd STEP [END of DEF 2.3]
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23 # [E] FORMAT MATCH NAME 3rd STEP [END of DEF 2.3]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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25 ### SPECIFICITY TBLASTX (/BLASTN) formatting:
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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26 ## 1/ "TBLASTX" formatting => At start of "RUN RUN RUN" change the keyword
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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27 ## 2/ change line "if keyword in nextline:" in function "split_file"
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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28 ## 3/ change "Strand" by "Frame" in function "get_information_on_matches"
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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31 ############################
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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32 ### DEF4 : get sequences ###
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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33 ############################
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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34 ### [+ get informations from the DEF3.]
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35 def get_sequences(query, list2, SUBMATCHEU, WORK_DIR):
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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36 list_Pairwise = []
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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38 F7 = open("%s/blastRun3.tmp" %WORK_DIR, 'w')
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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39 F7.write(bash1[query]) # bash1[query] ==> blast output for each query
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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40 F7.close()
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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41 F8 = open("%s/blastRun3.tmp" %WORK_DIR, 'r')
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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43 text1 = F8.readlines()
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45 miniList = []
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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46 for name in list2: # "list2" contains name of matched sequences (long version! the list1 is the same list but for short version names). It was previously generated by "detect_Matches" function
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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48 l = -1
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49 for n in text1:
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50 l = l+1
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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51 if name in n:
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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52 i = l
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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53 miniList.append(i) # content positions in the list "text1", of all begining of match (e.g. >gnl|UG|Apo#S51012099 [...])
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55 miniList.reverse()
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57 if miniList != []:
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58 length = len(miniList)
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60 ii = 0
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61 Listing1 = []
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62 while ii < length:
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63 iii = miniList[ii]
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64 entry = text1[iii:]
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65 text1 = text1[:iii]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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66 Listing1.append(entry) # each "entry" = list of thing beginning by ">"
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67 ii = ii+1 # Listing1 is a table of table!!
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69 Listing1.append(text1) # "text1" = the first lines (begin with "BLASTN 2.2.1 ...]"
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70 Listing1.reverse()
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72 Listing2 = Listing1[1:] # remove the first thing ("BLASTN ...") and keep only table beginning with a line with ">"
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73 SEK = len(Listing2)
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74 NB_SEK = 0
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75
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76 for e1 in Listing2: # "Listing2" contents all the entries begining with ">"
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77 NB_SEK = NB_SEK + 1
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78 list51 = []
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80 l = -1
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81 for line in e1:
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82 l = l+1
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83 if "Score =" in line:
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84 index = l
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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85 list51.append(l) # index of the lines with score
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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86
4
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87 list51.reverse()
1
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88 Listing3 = []
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89
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90 for i5 in list51:
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91 e2 = e1[i5:]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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92 Listing3.append(e2)
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93 e1 = e1[:i5]
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96 ######################################
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97 ### [C] FORMAT MATCH NAME 2nd STEP ###
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98
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diff changeset
99 BigFastaName = e1 ### LIST OF LINES <=> What is remaining after removing all the hit with "Score =", so all the text comprise between ">" and the first "Score =" ==> Include Match name & "Length & empty lines
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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diff changeset
100
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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diff changeset
101 SmallFastaName = BigFastaName[0] ## First line <=> MATCH NAME
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102
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lecorguille
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diff changeset
103 SmallFastaName = SmallFastaName[1:-2] ### remove ">" and "\n"
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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104
4
6709645eff5d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
105 """
6709645eff5d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
106 3 lines below : only difference with S05
6709645eff5d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
107 """
1
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
108 S1 = string.split(SmallFastaName, "||")
4
6709645eff5d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
parents: 1
diff changeset
109 S2 = string.split(S1[0], " ")
1
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
110 PutInFastaName1 = S2[0]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
111
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lecorguille
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diff changeset
112 ### [C] END FORMAT MATCH NAME 2nd STEP ###
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
113 ##########################################
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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114
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lecorguille
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115 SUBSEK = len(Listing3)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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116 NB_SUBSEK = 0
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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117 list_inBatch = []
4
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abims-sbr
parents: 1
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118
1
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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119 ### IF NO SUBMATCH WANTED !!!! => ONLY KEEP THE FIRST HIT OF "LISTING3":
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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120 if SUBMATCHEU == 0: # NO SUBMATCH WANTED !!!!
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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121 Listing4 = []
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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122 Listing4.append(Listing3[-1]) # Remove this line if submatch wanted!!!
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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123 elif SUBMATCHEU == 1:
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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124 Listing4 = Listing3
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125
4
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abims-sbr
parents: 1
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126 for l in Listing4: ## "listing3" contents
1
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lecorguille
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127 NB_SUBSEK = NB_SUBSEK+1
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128
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129 ll1 = string.replace(l[0], " ", "")
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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130 ll2 = string.replace(l[1], " ", "")
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
131 ll3 = string.replace(l[2], " ", "")
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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132 PutInFastaName2 = ll1[:-1] + "||" + ll2[:-1] + "||" + ll3[:-1] # match information
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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133
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134 seq_query = ""
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
135 pos_query = []
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
136 seq_match = ""
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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137 pos_match = []
4
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parents: 1
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138
1
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
139 for line in l:
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
140 if "Query:" in line:
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
141 line = string.replace(line, " ", " ") # remove multiple spaces in line
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
142 line = string.replace(line, " ", " ")
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
143 line = string.replace(line, " ", " ")
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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144
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lecorguille
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145 lll1 = string.split(line, " ") # split the line, 0: "Query=", 1:start, 2:seq, 3:end
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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146
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lecorguille
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147 pos1 = lll1[1]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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148 pos1 = string.atoi(pos1)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
149 pos_query.append(pos1)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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150
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lecorguille
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151 pos2 = lll1[3][:-1]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
152 pos2 = string.atoi(pos2)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
153 pos_query.append(pos2)
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154
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lecorguille
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155 seq = lll1[2]
4
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abims-sbr
parents: 1
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156 seq_query = seq_query + seq
1
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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diff changeset
157
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lecorguille
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diff changeset
158 if "Sbjct:" in line:
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
159 line = string.replace(line, " ", " ") # remove multiple spaces in line
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
160 line = string.replace(line, " ", " ")
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
161 line = string.replace(line, " ", " ")
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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diff changeset
162
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lecorguille
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163 lll2 = string.split(line, " ") # split the line, 0: "Query=", 1:start, 2:seq, 3:end
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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164
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lecorguille
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165 pos1 = lll2[1]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
166 pos1 = string.atoi(pos1)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
167 pos_match.append(pos1)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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168
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lecorguille
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diff changeset
169 pos2 = lll2[3][:-1]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
170 pos2 = string.atoi(pos2)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
171 pos_match.append(pos2)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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172
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lecorguille
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diff changeset
173 seq = lll2[2]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
174 seq_match = seq_match + seq
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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diff changeset
175
4
6709645eff5d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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176 ## Get the query and matched sequences and the corresponding positions
1
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lecorguille
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diff changeset
177 pos_query.sort() # rank small to big
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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178 pos_query_start = pos_query[0] # get the smaller
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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179 pos_query_end = pos_query[-1] # get the bigger
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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180 PutInFastaName3 = "%d...%d" %(pos_query_start, pos_query_end)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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181
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lecorguille
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182 ######################################
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lecorguille
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diff changeset
183 ### [D] FORMAT QUERY NAME 2nd STEP ###
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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184
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lecorguille
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diff changeset
185 FINAL_fasta_Name_Query = ">" + query + "||"+ PutInFastaName3 + "||[[%d/%d]][[%d/%d]]" %(NB_SEK, SEK, NB_SUBSEK,SUBSEK)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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186
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187 ### [D] END FORMAT QUERY NAME 2nd STEP ###
4
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188 ##########################################
1
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189
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lecorguille
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diff changeset
190 pos_match.sort()
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lecorguille
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191 pos_match_start = pos_match[0]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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192 pos_match_end = pos_match[-1]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
193 PutInFastaName4 = "%d...%d" %(pos_match_start, pos_match_end)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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194
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195 ######################################
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lecorguille
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diff changeset
196 ### [E] FORMAT MATCH NAME 3rd STEP ###
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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197
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198 FINAL_fasta_Name_Match = ">" + PutInFastaName1 + "||" + PutInFastaName4 + "||[[%d/%d]][[%d/%d]]" %(NB_SEK, SEK, NB_SUBSEK,SUBSEK)
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199
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200 ### [E] END FORMAT MATCH NAME 3rd STEP ###
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201 ##########################################
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202
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203 Pairwise = [FINAL_fasta_Name_Query , seq_query , FINAL_fasta_Name_Match , seq_match] # list with 4 members
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204 list_Pairwise.append(Pairwise)
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205
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206 ### Get informations about matches
4
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207 list_info = get_information_on_matches(l) ### DEF3 ###
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208
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209 F8.close()
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210 return(list_Pairwise, list_info)
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211 #########################################
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212
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213
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214 ###################
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215 ### RUN RUN RUN ###
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216 ###################
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217 import string, os, time, re, sys
4
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218 from functions import split_file, detect_Matches, get_information_on_matches
1
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219
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220 ## 1 ## INPUT/OUTPUT
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221 SHORT_FILE = sys.argv[1] ## short-name-query_short-name-db
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222
4
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223 """
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224 04 and 06 for S05, 11 and 13 for S08
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225 """
1
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226 path_in = "%s/11_outputBlast_%s.txt" %(SHORT_FILE, SHORT_FILE)
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227 file_out = open("%s/13_PairwiseMatch_%s.fasta" %(SHORT_FILE, SHORT_FILE),"w")
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228
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229 ## 2 ## RUN
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230 ## create Bash1 ##
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231 bash1 = split_file(path_in, "TBLASTX") ### DEF1 ###
1
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232
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233 ## detect and save match ##
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234 list_hits =[]
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235 list_no_hits = []
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236 j= 0
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237 k = 0
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238 lene = len(bash1.keys())
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239 for query in bash1.keys():
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240 j = j+1
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241
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242 ## 2.1. detect matches ##
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243 list_match, list_match2, hit=detect_Matches(query, MATCH, SHORT_FILE, bash1) ### DEF2 ###
1
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244
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245 if hit == 1: # match(es)
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246 list_hits.append(query)
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247 if hit == 0: # no match for that sequence
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248 list_no_hits.append(query)
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249
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250 ## 2.2. get sequences ##
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251 if hit ==1:
4
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252 list_pairwiseMatch, list_info = get_sequences(query, list_match2, SUBMATCH, SHORT_FILE)
1
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253
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254 # divergencve
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255 divergence = list_info[6]
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256 # gap number
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257 gap_number = list_info[7]
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258 # real divergence (divergence without accounting INDELs)
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259 real_divergence = list_info[8]
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260 # length matched
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261 length_matched = list_info[10]
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262
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263 ### WRITE PAIRWISE ALIGNMENT IN OUTPUT FILES
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264 for pairwise in list_pairwiseMatch:
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265 k = k+1
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266
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267 query_name = pairwise[0]
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268 query_seq = pairwise[1]
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269 match_name = pairwise[2]
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270 match_seq = pairwise[3]
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271
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272 len_query_seq = len(query_seq)
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273
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274 # If NO CONTROL FOR LENGTH, USE THE FOLLOWING LINES INSTEAD:
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275
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276 file_out.write("%s||%s||%s||%s||%s" %(query_name,divergence,gap_number,real_divergence,length_matched))
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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277 file_out.write("\n")
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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278 file_out.write("%s" %query_seq)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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279 file_out.write("\n")
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280
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281 file_out.write("%s||%s||%s||%s||%s" %(match_name,divergence,gap_number,real_divergence,length_matched))
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282 file_out.write("\n")
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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283 file_out.write("%s" %match_seq)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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284 file_out.write("\n")
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285
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286
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287 file_out.close()