Mercurial > repos > abims-sbr > pairwise

annotate scripts/S06_post_processing_of_pairwise.py @ 4:6709645eff5d draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
author abims-sbr
date Wed, 17 Jan 2018 08:53:53 -0500
parents c8af52875b0f
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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
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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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6709645eff5d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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5 MINIMUM_LENGTH = 1
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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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7 #######################
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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8 ##### RUN RUN RUN #####
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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9 #######################
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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10 import string, os, time, re, sys
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6709645eff5d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
abims-sbr
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11 from functions import get_pairs, extract_length, filter_redondancy
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c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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13 ## 1 ## INPUT/OUTPUT
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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14 SHORT_FILE = sys.argv[1] #short-name-query_short-name-db
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 F_IN = "%s/06_PairwiseMatch_%s.fasta" %(SHORT_FILE, SHORT_FILE)
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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18 F_OUT = "%s/09_PairwiseMatch_filtered_%s.fasta" %(SHORT_FILE, SHORT_FILE)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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19 File_OUT = open(F_OUT, "w")
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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21 F_OUT2 = "%s/09_onlyMatch_filtered_%s.fasta" %(SHORT_FILE, SHORT_FILE)
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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22 File_OUT2 = open(F_OUT2, "w")
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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24 ## 2 ## RUN
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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25 list_pairwises = get_pairs(F_IN) ### DEF1 ###
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6709645eff5d planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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26 list_pairwises_filtered1 = filter_redondancy(list_pairwises, MINIMUM_LENGTH) ### DEF3 ###
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c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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28 i = 0
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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29 for pair in list_pairwises_filtered1:
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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30 i = i+1
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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32 ## Write pairwise alignment
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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33 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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34 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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35 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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36 File_OUT.write("%s\n" %pair[3])
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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38 ## Write only "matches" [AND UNGAP THEM: needed before the 2nd run of blast]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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39 File_OUT2.write("%s\n" %pair[2])
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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40 seq_match = pair[3]
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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41 seq_match_ungapped = string.replace(seq_match, "-", "")
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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42 File_OUT2.write("%s\n" %seq_match_ungapped)
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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44 File_OUT.close()
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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45 File_OUT2.close()