Mercurial > repos > abims-sbr > concatphyl

annotate scripts/S01_concatenate.py @ 1:f181bd945a6c draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
author lecorguille
date Thu, 13 Apr 2017 09:48:47 -0400
parents
children 1f8d039bd241
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
1 #!/usr/bin/python
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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2 ## Author: Eric Fontanillas
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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3 ## Last modification: 17/06/2011
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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4 ## Subject: find and remove indels
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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5
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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6
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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7 ###############################
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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8 ##### DEF 0 : Dico fasta #####
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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9 ###############################
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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10 def dico(F2):
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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11 dicoco = {}
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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12 while 1:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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13 next2 = F2.readline()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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14 if not next2:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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15 break
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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16 if next2[0] == ">":
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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17 fasta_name_query = next2[:-1]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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18 Sn = string.split(fasta_name_query, "||")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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19 fasta_name_query = Sn[0]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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20 next3 = F2.readline()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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21 fasta_seq_query = next3[:-1]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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22 dicoco[fasta_name_query]=fasta_seq_query
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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23 return(dicoco)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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24 ###################################################################################
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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26
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lecorguille
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27 ####################
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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28 ###### DEF 11 ######
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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29 ####################
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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30 ## Concatenate sequences
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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31 ###########################
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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32 def concatenate(folder_with_loci, SPECIES_ID_LIST):
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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33 ## 4 ## Process files
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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34 ## 4.1 ## Create the bash and the fasta names entries (name of the species)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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35 bash_concat = {}
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36
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lecorguille
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37 for species_ID in SPECIES_ID_LIST:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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38 bash_concat[species_ID] = ''
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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39
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lecorguille
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40 ln_concat = 0
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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41 nb_locus = 0
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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42 pos=1
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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43 list_genes_position=[]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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44 ## 4.2 ## Concatenate
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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45 for file in L_IN:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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46 nb_locus=nb_locus+1
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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47
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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48 ## a ## Open alignments
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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49 file_IN = open("%s/%s" %(folder_with_loci, file), "r")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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50 dico_seq = dico(file_IN) ### DEF 0 ###
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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51 file_IN.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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52 ## b ## Get alignment length + genes positions for RAxML
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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53 key0 = dico_seq.keys()[0]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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54 ln = len(dico_seq[key0])
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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55 ln_concat = ln_concat + ln
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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56
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57 pos_start = pos
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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58 pos_end = pos+ln-1
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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59 pos=pos_end+1
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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60 position="%d-%d" %(pos_start, pos_end)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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61 RAxML_name = file[:-6]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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62 sublist = [RAxML_name, position]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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63 list_genes_position.append(sublist)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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64
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65 ## c ## Generate "empty" sequence with alignment length * "-"
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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66 empty_seq = "-" * ln
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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67
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lecorguille
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68 ## d ## Concatenate
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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69 ## d.1 ## Detect missing species in this alignment
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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70 list_ID=[]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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71 list_absent_ID=[]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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72 bash_fastaName={}
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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73 for fasta_name in dico_seq:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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74 ID = fasta_name[1:3]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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75 list_ID.append(ID)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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76 seq = dico_seq[fasta_name]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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77 bash_fastaName[ID]=fasta_name
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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78 for sp_ID in SPECIES_ID_LIST:
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lecorguille
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79 if sp_ID not in list_ID:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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80 list_absent_ID.append(sp_ID)
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81
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82 for ID in SPECIES_ID_LIST:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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83 if ID in list_absent_ID:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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84 bash_concat[ID] = bash_concat[ID] + empty_seq
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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85 else:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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86 fasta_name = bash_fastaName[ID]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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87 seq = dico_seq[fasta_name]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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88 bash_concat[ID] = bash_concat[ID] + seq
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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89
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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90 return(bash_concat, ln_concat, nb_locus, list_genes_position)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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91 ####################################
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92
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93
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94 ########################################
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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95 ##### DEF 12 : get codon position #####
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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96 ########################################
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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97 def get_codon_position(seq_inORF):
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98
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99 ln = len(seq_inORF)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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100
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101 i=0
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lecorguille
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102 seq_pos1=""
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
103 seq_pos2=""
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
104 seq_pos12=""
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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diff changeset
105 seq_pos3=""
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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106 while i<ln:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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107 pos1 = seq_inORF[i]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
108 pos2 = seq_inORF[i+1]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
109 pos3 = seq_inORF[i+2]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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110
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111 seq_pos1 = seq_pos1 + pos1
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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112 seq_pos2 = seq_pos2 + pos2
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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113 seq_pos12 = seq_pos12 + pos1 + pos2
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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114 seq_pos3 = seq_pos3 + pos3
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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115
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116 i = i+3
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117
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118 return(seq_pos1, seq_pos2, seq_pos12, seq_pos3)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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119 ###############################################################################
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120
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121
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122
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lecorguille
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123 #######################
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lecorguille
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124 ##### RUN RUN RUN #####
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lecorguille
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125 #######################
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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126 import string, os, time, re, sys, zipfile
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127
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128 list_species = []
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129 SPECIES_ID_LIST = []
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130 fasta = "^.*fasta$"
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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131 i=3
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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132
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133 ## add file to list_species
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134 zfile = zipfile.ZipFile(sys.argv[1])
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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135 for name in zfile.namelist() :
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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136 list_species.append(name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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137
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138 ## in SPECIES_ID_LIST, only the 2 first letters of name of species
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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139 for name in list_species :
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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140 name = name[:2]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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141 SPECIES_ID_LIST.append(name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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142
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143
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lecorguille
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144 ### 1 ### Proteic
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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145 if sys.argv[2] == "proteic" :
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lecorguille
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146 os.mkdir("02_CDS_No_Missing_Data_aa")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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147 zfile_nuc = zipfile.ZipFile(sys.argv[3])
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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148 for name in zfile_nuc.namelist() :
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lecorguille
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149 zfile_nuc.extract(name, "./02_CDS_No_Missing_Data_aa")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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150 path_IN = "./02_CDS_No_Missing_Data_aa"
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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151 L_IN = os.listdir(path_IN)
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152
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153 OUT1 = open("02_Concatenation_aa.fas", "w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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154 OUT2 = open("02_Concatenation_aa.phy", "w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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155 OUT3 = open("02_Concatenation_aa.nex", "w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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156 OUT_PARTITION_gene_AA = open("06_partitions_gene_AA","w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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157
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158
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lecorguille
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159 ## Get bash with concatenation
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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160 bash_concatenation, ln, nb_locus,list_genes_position= concatenate(path_IN, SPECIES_ID_LIST) ### DEF 11 ##
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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161
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162 ## Write gene AA partition file for RAxML
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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163 for sublist in list_genes_position:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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164 name = sublist[0]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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165 positions=sublist[1]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
166 OUT_PARTITION_gene_AA.write("DNA,%s=%s\n"%(name,positions))
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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167 OUT_PARTITION_gene_AA.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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168
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parents:
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169 ## Get "ntax" for NEXUS HEADER
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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170 nb_taxa = len(bash_concatenation.keys())
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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171
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lecorguille
parents:
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172 print "******************** CONCATENATION ********************\n"
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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173 print "Process amino-acid concatenation:"
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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174 print "\tNumber of taxa aligned = %d" %nb_taxa
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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175 print "\tNumber of loci concatenated = %d\n" %nb_locus
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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176 print "\tTotal length of the concatenated sequences = %d" %ln
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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177
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178
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parents:
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179 ## Print NEXUS HEADER:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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180 OUT3.write("#NEXUS\n\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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181 OUT3.write("Begin data;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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182 OUT3.write("\tDimensions ntax=%d nchar=%d;\n" %(nb_taxa, ln))
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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183 OUT3.write("\tFormat datatype=aa gap=-;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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184 OUT3.write("\tMatrix\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
diff changeset
185
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lecorguille
parents:
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186 ## Print PHYLIP HEADER:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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187 OUT2.write(" %d %d\n" %(nb_taxa, ln))
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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188
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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diff changeset
189 ## 3.5 ## Print outputs
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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190 for seq_name in bash_concatenation.keys():
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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191 seq = bash_concatenation[seq_name]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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192
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193 ## Filtering the sequence in case of remaining "?"
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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194 seq = string.replace(seq, "?", "-")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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195
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196 #print seq FASTA FORMAT
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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197 OUT1.write(">%s\n" %seq_name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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198 OUT1.write("%s\n" %seq)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
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199
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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parents:
diff changeset
200 #print seq PHYLIP FORMAT
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
201 OUT2.write("%s\n" %seq_name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
202 OUT2.write("%s\n" %seq)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
203
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
204 #print seq NEXUS FORMAT
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
205 OUT3.write("%s" %seq_name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
206 OUT3.write(" %s\n" %seq)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
207
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
208 OUT3.write("\t;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
209 OUT3.write("End;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
210 OUT1.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
211 OUT2.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
212 OUT2.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
213
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
214
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
215 ### 2 ### Nucleic
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
216 elif sys.argv[2] == "nucleic" :
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
217 os.mkdir("02_CDS_No_Missing_Data_nuc")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
218
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
219 zfile_nuc = zipfile.ZipFile(sys.argv[3])
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
220 for name in zfile_nuc.namelist() :
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
221 zfile_nuc.extract(name, "./02_CDS_No_Missing_Data_nuc")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
222 path_IN = "./02_CDS_No_Missing_Data_nuc"
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
223 L_IN = os.listdir(path_IN)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
224
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
225 OUT1 = open("03_Concatenation_nuc.fas", "w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
226 OUT2 = open("03_Concatenation_nuc.phy", "w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
227 OUT3 = open("03_Concatenation_nuc.nex", "w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
228
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
229 OUT1_pos12 = open("03_Concatenation_pos12_nuc.fas", "w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
230 OUT2_pos12 = open("03_Concatenation_pos12_nuc.phy", "w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
231 OUT3_pos12 = open("03_Concatenation_pos12_nuc.nex", "w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
232
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
233 OUT1_pos3 = open("03_Concatenation_pos3_nuc.fas", "w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
234 OUT2_pos3 = open("03_Concatenation_pos3_nuc.phy", "w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
235 OUT3_pos3 = open("03_Concatenation_pos3_nuc.nex", "w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
236
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
237 OUT_PARTITION_codon_12_3 = open("05_partitions_codon12_3","w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
238 OUT_PARTITION_gene_NUC = open("05_partitions_gene_NUC","w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
239 OUT_PARTITION_gene_PLUS_codon_12_3 = open("05_partitions_gene_PLUS_codon12_3","w")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
240
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
241 ## Get bash with concatenation
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
242 bash_concatenation, ln, nb_locus, list_genes_position = concatenate(path_IN, SPECIES_ID_LIST) ### DEF 11 ##
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
243 ln_12 = ln/3*2 ### length of the alignment when only the 2 first codon position
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
244 ln_3 = ln/3 ### length of the alignment when only the third codon position
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
245
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
246 ## Write partition files for RAxML subsequent runs
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
247 # a # Codon partition
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
248 OUT_PARTITION_codon_12_3.write("DNA, p1=1-%d\\3,2-%d\\3\n" %(ln, ln))
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
249 OUT_PARTITION_codon_12_3.write("DNA, p2=3-%d\\3\n" %(ln))
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
250 OUT_PARTITION_codon_12_3.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
251
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
252 # b # Gene partition
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
253 for sublist in list_genes_position:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
254 name=sublist[0]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
255 positions=sublist[1]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
256 OUT_PARTITION_gene_NUC.write("DNA,%s=%s\n"%(name,positions))
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
257 OUT_PARTITION_gene_NUC.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
258
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
259 # c # Mixed partition (codon + gene)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
260 for sublist in list_genes_position:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
261 name = sublist[0]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
262 positions = sublist[1]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
263 S1 = string.split(positions, "-")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
264 pos_start1 = string.atoi(S1[0])
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
265 pos_end = string.atoi(S1[1])
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
266 pos_start2=pos_start1+1
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
267 pos_start3=pos_start2+1
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
268 partition1 = "DNA, %s_1=%d-%d\\3,%d-%d\\3\n" %(name,pos_start1, pos_end, pos_start2, pos_end)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
269 partition2 = "DNA, %s_2=%d-%d\\3\n" %(name,pos_start3, pos_end)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
270 OUT_PARTITION_gene_PLUS_codon_12_3.write(partition1)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
271 OUT_PARTITION_gene_PLUS_codon_12_3.write(partition2)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
272
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
273 OUT_PARTITION_gene_PLUS_codon_12_3.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
274
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
275
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
276 ## Get "ntax" for NEXUS HEADER
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
277 nb_taxa = len(bash_concatenation.keys())
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
278
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
279 print "******************** CONCATENATION ********************\n"
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
280 print "Process nucleotides concatenation:"
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
281 print "\tNumber of taxa aligned = %d" %nb_taxa
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
282 print "\tNumber of loci concatenated = %d\n" %nb_locus
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
283 print "\tTotal length of the concatenated sequences [All codon positions] = %d" %ln
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
284 print "\t\tTotal length of the concatenated sequences [Codon positions 1 & 2] = %d" %ln_12
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
285 print "\t\tTotal length of the concatenated sequences [Codon position 3] = %d" %ln_3
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
286
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
287
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
288 ## Print NEXUS HEADER:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
289 OUT3.write("#NEXUS\n\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
290 OUT3.write("Begin data;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
291 OUT3.write("\tDimensions ntax=%d nchar=%d;\n" %(nb_taxa, ln))
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
292 OUT3.write("\tFormat datatype=dna gap=-;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
293 OUT3.write("\tMatrix\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
294
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
295 OUT3_pos12.write("#NEXUS\n\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
296 OUT3_pos12.write("Begin data;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
297 OUT3_pos12.write("\tDimensions ntax=%d nchar=%d;\n" %(nb_taxa, ln_12))
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
298 OUT3_pos12.write("\tFormat datatype=dna gap=-;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
299 OUT3_pos12.write("\tMatrix\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
300
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
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301 OUT3_pos3.write("#NEXUS\n\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
302 OUT3_pos3.write("Begin data;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
303 OUT3_pos3.write("\tDimensions ntax=%d nchar=%d;\n" %(nb_taxa, ln_3))
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
304 OUT3_pos3.write("\tFormat datatype=dna gap=-;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
305 OUT3_pos3.write("\tMatrix\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
306
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
307 ## Print PHYLIP HEADER:
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
308 OUT2.write(" %d %d\n" %(nb_taxa, ln))
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
309 OUT2_pos12.write(" %d %d\n" %(nb_taxa, ln_12))
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
310 OUT2_pos3.write(" %d %d\n" %(nb_taxa, ln_3))
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
311
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
312 ## Print outputs
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
313 for seq_name in bash_concatenation.keys():
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
314 seq = bash_concatenation[seq_name]
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
315
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
316 ## Filtering the sequence in case of remaining "?"
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
317 seq = string.replace(seq, "?", "-")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
318
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
319 ## Get the differentes codons partitions
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
320 seq_pos1, seq_pos2, seq_pos12, seq_pos3 = get_codon_position(seq) ### DEF 12 ###
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
321
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
322 #print seq FASTA FORMAT
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
323 OUT1.write(">%s\n" %seq_name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
324 OUT1.write("%s\n" %seq)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
325 OUT1_pos12.write(">%s\n" %seq_name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
326 OUT1_pos12.write("%s\n" %seq_pos12)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
327 OUT1_pos3.write(">%s\n" %seq_name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
328 OUT1_pos3.write("%s\n" %seq_pos3)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
329
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
330 #print seq PHYLIP FORMAT
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
331 OUT2.write("%s\n" %seq_name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
332 OUT2.write("%s\n" %seq)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
333 OUT2_pos12.write("%s\n" %seq_name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
334 OUT2_pos12.write("%s\n" %seq_pos12)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
335 OUT2_pos3.write("%s\n" %seq_name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
336 OUT2_pos3.write("%s\n" %seq_pos3)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
337
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
338 #print seq NEXUS FORMAT
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
339 OUT3.write("%s" %seq_name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
340 OUT3.write(" %s\n" %seq)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
341 OUT3_pos12.write("%s" %seq_name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
342 OUT3_pos12.write(" %s\n" %seq_pos12)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
343 OUT3_pos3.write("%s" %seq_name)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
344 OUT3_pos3.write(" %s\n" %seq_pos3)
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
345
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
346
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
347 OUT3.write("\t;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
348 OUT3.write("End;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
349 OUT3_pos12.write("\t;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
350 OUT3_pos12.write("End;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
351 OUT3_pos3.write("\t;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
352 OUT3_pos3.write("End;\n")
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
353
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
354 OUT1.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
355 OUT2.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
356 OUT3.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
357 OUT1_pos12.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
358 OUT2_pos12.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
359 OUT3_pos12.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
360 OUT1_pos3.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
361 OUT2_pos3.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
362 OUT3_pos3.close()
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
363
f181bd945a6c planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
parents:
diff changeset
364 print "\n\n\n******************** RAxML RUN ********************\n"