Mercurial > repos > abims-sbr > cds_search
annotate scripts/S02_remove_too_short_bit_or_whole_sequence.py @ 1:c79bdda8abfb draft default tip
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3a118aa934e6406cc8b0b24d006af6365c277519
author | abims-sbr |
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date | Thu, 09 Jun 2022 12:40:00 +0000 |
parents | eb95bf7f90ae |
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rev | line source |
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eb95bf7f90ae
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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1 #!/usr/bin/env python |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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2 # coding: utf8 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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3 ## Author: Eric Fontanillas |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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4 ## Modification: 03/09/14 by Julie BAFFARD |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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5 ## Last modification : 05/03/18 by Victor Mataigne |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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6 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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7 ## Description : find and remove indels |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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8 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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9 ################### |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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10 ###### DEF 9 ###### |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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11 ################### |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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12 def detect_short_indel(seq,MAX_LENGTH_SMALL_INDEL): |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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13 ## 1 ## Built the list of sublist of consecutive gap position |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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14 LIST = [] |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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15 sublist=[] |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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16 ln = len(seq) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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17 i=0 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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18 while i < ln: |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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19 if seq[i] == "-": |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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20 sublist.append(i) ## save gaps in sublist until a aa is found => else: |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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21 else: |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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22 LIST.append(sublist) ## save the list of gap |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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23 sublist = [] ## create new list of gap |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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24 i = i+1 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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25 ## if gap at the end: add the last "sublist of gap" (not done in previous loop, at it add sublist (of gaps) only when in find aa, but if gap at the end, no aa after are present, so cannot add this last sublist to the LISt of gaps |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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26 if sublist != []: |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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27 LIST.append(sublist) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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28 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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29 ## 2 ## keep only the records of the small indel (<MAX_LENGTH_SMALL_INDEL) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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30 list_of_sublist_positions = [] |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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31 for element in LIST: |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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32 if element != [] and len(element)<=MAX_LENGTH_SMALL_INDEL: |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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33 list_of_sublist_positions.append(element) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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34 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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35 return(list_of_sublist_positions) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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36 #################################### |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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37 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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38 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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39 ####################### |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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40 ##### RUN RUN RUN ##### |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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41 ####################### |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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42 import string, os, time, re, sys |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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43 from dico import dico |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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44 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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45 ### 0 ### PARAMETERS |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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46 MIN_LENGTH_ALL_aa = int(sys.argv[3])-20 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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47 MIN_LENGTH_BIT_OF_SEQUENCE_aa = int(sys.argv[4]) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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48 MAX_LENGTH_SMALL_INDEL = 2 ## in aa |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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49 MAX_LENGTH_SMALL_INDEL_nuc = 6 ## in nuc |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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50 MIN_SPECIES_NB = int(sys.argv[1]) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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51 dicoco = {} |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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52 dico_dico = {} |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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53 list_new_file = [] |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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54 n0 = 0 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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55 e=0 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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56 j=0 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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57 i=1 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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58 name_elems = ["orthogroup", "0", "with", "0", "species.fasta"] |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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59 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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60 ### 1 ### IN |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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61 if sys.argv[2] == "oui" : |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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62 path_IN1 = "./06_CDS_with_M_aa/" |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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63 L_IN1 = os.listdir(path_IN1) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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64 path_IN2 = "./06_CDS_with_M_nuc/" |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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65 L_IN2 = os.listdir(path_IN2) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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66 elif sys.argv[2] == "non" : |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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67 path_IN1 = "./05_CDS_aa/" |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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68 L_IN1 = os.listdir(path_IN1) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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69 path_IN2 = "./05_CDS_nuc/" |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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70 L_IN2 = os.listdir(path_IN2) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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71 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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72 ## 2 ## OUT |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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73 os.mkdir("07_CDS_aa") |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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74 path_OUT1 = "07_CDS_aa" |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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75 os.mkdir("07_CDS_nuc") |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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76 path_OUT2 = "07_CDS_nuc" |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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77 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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78 for file in L_IN1: |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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79 file_INaa = "%s/%s" %(path_IN1, file) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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80 file_INnuc = "%s/%s" %(path_IN2, file) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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81 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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82 dico_aa = dico(file_INaa) ### DEF 0 ### |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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83 dico_nuc = dico(file_INnuc) ### DEF 0 ### |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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84 |
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85 new_bash_aa = {} |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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86 new_bash_nuc = {} |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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87 for fasta_name in dico_aa.keys(): |
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88 seq = dico_aa[fasta_name] |
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89 seq_nuc = dico_nuc[fasta_name] |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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90 |
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91 if "?" in seq: |
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92 seq = str.replace(seq, "?", "-") |
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93 if "?" in seq_nuc: |
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94 seq_nuc = str.replace(seq_nuc, "?", "-") |
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95 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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96 ## 4.1 ## [FILTER 1] : Detect and Replace short internal indel symbole (= "-" as for other longer gaps) by a "?" |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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97 ## aa |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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98 list_sublist_pos = detect_short_indel(seq, MAX_LENGTH_SMALL_INDEL) ### DEF 9 ### |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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99 for pos_short_indels in list_sublist_pos: |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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100 for pos in pos_short_indels: |
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101 seq = seq[:pos] + "?" + seq[pos+1:] |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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102 ## nuc |
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103 list_sublist_pos = detect_short_indel(seq_nuc, MAX_LENGTH_SMALL_INDEL_nuc) ### DEF 9 ### |
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104 for pos_short_indels in list_sublist_pos: |
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105 for pos in pos_short_indels: |
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106 seq_nuc = seq_nuc[:pos] + "?" + seq_nuc[pos+1:] |
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107 |
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108 ## 4.2 ## [FILTER 2] : Remove short bits of sequence (<"MIN_LENGTH_BIT_OF_SEQUENCE_aa") |
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109 LIST_sublist_aa=[] |
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110 S1 = str.split(seq, "-") |
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111 for element in S1: |
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112 if len(element) > MIN_LENGTH_BIT_OF_SEQUENCE_aa: |
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113 LIST_sublist_aa.append(element) |
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114 |
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115 ## 4.3 ## [FILTER 3] : Remove all the sequence if the total length of all subsequences < "MIN_LENGTH_ALL_aa") |
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116 seq_all = "" |
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117 for bit_of_sequence in LIST_sublist_aa: |
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118 seq_all = seq_all + bit_of_sequence |
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119 |
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120 if len(seq_all) < MIN_LENGTH_ALL_aa: |
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121 LIST_sublist_aa = [] |
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122 |
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123 ## 4.4 ## [FILTER 4] : Detect sublist position in the original sequence, and recreate the filtered sequence from these positions: |
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124 seq_gap = "-" * len(seq) ## 4.4.1 ## generate a sequence with only gaps inside |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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125 seq_gap_nuc = "-" * len(seq_nuc) |
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126 |
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127 for subsequence in LIST_sublist_aa: |
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128 ## aa |
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129 START = str.find(seq, subsequence) |
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130 END = START + len(subsequence) |
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131 seq_gap = seq_gap[:START] + seq[START:END] + seq_gap[END:] ## 4.4.2 ## and then replace the correponding gaps by coding subsequence in the sequence |
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132 ## nuc |
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133 START_nuc = START*3 |
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134 END_nuc = END*3 |
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135 seq_gap_nuc = seq_gap_nuc[:START_nuc] + seq_nuc[START_nuc:END_nuc] + seq_gap_nuc[END_nuc:] |
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136 |
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137 ## 4.5 ## Save new sequence in bash if not empty |
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138 seq_empty_test = str.replace(seq_gap, "-", "") |
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139 if seq_empty_test != "": |
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140 new_bash_aa[fasta_name] = seq_gap |
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141 |
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142 seq_empty_test = str.replace(seq_gap_nuc, "-", "") |
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143 if seq_empty_test != "": |
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144 new_bash_nuc[fasta_name] = seq_gap_nuc |
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145 |
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146 # 4.6 ## Correct the nb of sequence in the output name, if necessary |
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147 n0 += 1 |
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148 name_elems[1] = file.split('_')[1] |
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149 #name_elems[1] = str(n0) |
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150 name_elems[3] = str(len(new_bash_nuc.keys())) |
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151 new_name = "_".join(name_elems) |
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152 dico_dico[new_name] = [new_bash_aa, new_bash_nuc] |
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153 list_new_file.append(new_name) |
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154 |
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155 ## [FILTER 6]: print output only if at least "MIN_SPECIES_NB" species remaining in the alignment |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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156 for name in list_new_file : |
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157 dicoo = dico_dico[name] |
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158 dico_aa = dicoo[0] |
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159 dico_nuc = dicoo[1] |
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160 sp_nbre = len(dico_aa.keys()) |
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161 |
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162 if sp_nbre >= MIN_SPECIES_NB : |
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163 file_OUTaa = open("%s/%s" %(path_OUT1, name), "w") |
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164 file_OUTnuc = open("%s/%s" %(path_OUT2, name), "w") |
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165 |
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166 for fasta_name in dico_aa.keys() : |
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167 seq_aa = dico_aa[fasta_name] |
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168 file_OUTaa.write("%s\n" %fasta_name) |
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169 file_OUTaa.write("%s\n" %seq_aa) |
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170 for fasta_name in dico_nuc.keys() : |
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171 seq_nuc = dico_nuc[fasta_name] |
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172 file_OUTnuc.write("%s\n" %fasta_name) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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173 file_OUTnuc.write("%s\n" %seq_nuc) |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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174 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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175 file_OUTaa.close() |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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176 file_OUTnuc.close() |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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177 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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178 else: |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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179 e+=1 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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180 |
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181 ###Print |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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182 if sys.argv[2] == "oui" : |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3a118aa934e6406cc8b0b24d006af6365c277519
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183 print("\nIn locus with CDS considering Methionine : \n") |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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184 else : |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3a118aa934e6406cc8b0b24d006af6365c277519
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185 print("\nIn locus with CDS regardless of the Methionine : \n") |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty
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186 |
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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3a118aa934e6406cc8b0b24d006af6365c277519
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187 print("\nTotal number of locus recorded = %d" %n0) |