Mercurial > repos > abims-sbr > pairwise

annotate scripts/S06_post_processing_of_pairwise.py @ 1:c8af52875b0f draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
author lecorguille
date Thu, 13 Apr 2017 09:46:45 -0400
parents
children 6709645eff5d
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c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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1 #!/usr/bin/env python
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
lecorguille
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2 ## AUTHOR: Eric Fontanillas
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3 ## LAST VERSION: 14/08/14 by Julie BAFFARD
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5 MINIMUM_LENGTH = 1 #bp
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8 ############################
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9 ##### DEF1 : Get Pairs #####
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10 ############################
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11 def get_pairs(fasta_file_path):
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12 F2 = open(fasta_file_path, "r")
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13 list_pairwises = []
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14 while 1:
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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15 next2 = F2.readline()
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16 if not next2:
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17 break
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18 if next2[0] == ">":
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19 fasta_name_query = next2[:-1]
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20 next3 = F2.readline()
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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21 fasta_seq_query = next3[:-1]
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22 next3 = F2.readline() ## jump one empty line (if any after the sequence)
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23 fasta_name_match = next3[:-1]
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24 next3 = F2.readline()
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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25 fasta_seq_match = next3[:-1]
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26 pairwise = [fasta_name_query,fasta_seq_query,fasta_name_match,fasta_seq_match]
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28 ## ADD pairwise with condition
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29 list_pairwises.append(pairwise)
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30 F2.close()
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32 return(list_pairwises)
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33 ##############################################
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34
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35 #################################
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36 ##### DEF2 : Extract length #####
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37 #################################
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38 def extract_length(length_string): # format length string = 57...902
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39 l3 = string.split(length_string, "...")
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40 n1 = string.atoi(l3[0])
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41 n2 = string.atoi(l3[1])
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42 length = n2-n1
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44 return(length)
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45 ##############################################
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48 ####################################
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49 ##### DEF3 : Remove Redondancy #####
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50 ####################################
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51 def filter_redondancy_and_length(list_paireu, MIN_LENGTH):
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53 bash1 = {}
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54 list_pairout = []
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56 for pair in list_paireu:
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57 query_name = pair[0]
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58 query_seq = pair[1]
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59 match_name = pair[2]
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60 match_seq = pair[3]
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61
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62 l1 = string.split(query_name, "||")
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63 short_query_name = l1[0][1:]
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64 length_matched = extract_length(l1[1]) ### DEF2 ###
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65 l2 = string.split(match_name, "||")
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66 short_match_name = l2[0][1:]
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67 binom = "%s_%s" %(short_query_name, short_match_name)
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68
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69 ## TEST FOR REDONDANCY
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70 ## REDONDANCY OF BINOME!!!! => MATCHE BETWEEN THE SAME 2 CONTIGS, BUT AT DIFFERENT POSITIONS ON THE CONTIG
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71 ## REDONDANCY NOT REMOVED HERE:
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72 ## 1/ Several "TERA" match with one "APN" (Counted in script "09_formatMatch_getBackNucleotides.py")
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73 ## 2/ Several "APN" match with one "TERA" (Counted
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74 if binom not in bash1.keys():
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75 bash1[binom] = [query_name, query_seq, match_name, match_seq, length_matched]
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76 else:
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77 old_length = bash1[binom][-1]
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78 if length_matched > old_length:
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79 bash1[binom] = [query_name, query_seq, match_name, match_seq, length_matched]
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81
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82 for bino in bash1.keys():
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83 length = bash1[bino][-1]
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84 if length > MIN_LENGTH:
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85 list_pairout.append(bash1[bino])
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86
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87 return(list_pairout)
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88 ##############################################
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90
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91 #######################
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92 ##### RUN RUN RUN #####
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93 #######################
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94 import string, os, time, re, sys
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95
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96 ## 1 ## INPUT/OUTPUT
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97 SHORT_FILE = sys.argv[1] #short-name-query_short-name-db
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98
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99 F_IN = "%s/06_PairwiseMatch_%s.fasta" %(SHORT_FILE, SHORT_FILE)
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100
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101 F_OUT = "%s/09_PairwiseMatch_filtered_%s.fasta" %(SHORT_FILE, SHORT_FILE)
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102 File_OUT = open(F_OUT, "w")
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103
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104 F_OUT2 = "%s/09_onlyMatch_filtered_%s.fasta" %(SHORT_FILE, SHORT_FILE)
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105 File_OUT2 = open(F_OUT2, "w")
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106
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107 ## 2 ## RUN
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108 list_pairwises = get_pairs(F_IN) ### DEF1 ###
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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109 list_pairwises_filtered1 = filter_redondancy_and_length(list_pairwises, MINIMUM_LENGTH) ### DEF3 ###
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110
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111 i = 0
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112 for pair in list_pairwises_filtered1:
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113 i = i+1
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114
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115 ## Write pairwise alignment
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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116 File_OUT.write("%s\n" %pair[0])
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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117 File_OUT.write("%s\n" %pair[1])
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118 File_OUT.write("%s\n" %pair[2])
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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119 File_OUT.write("%s\n" %pair[3])
c8af52875b0f planemo upload for repository https://github.com/abims-sbr/adaptsearch commit ab76075e541dd7ece1090f6b55ca508ec0fde39d
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120
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121 ## Write only "matches" [AND UNGAP THEM: needed before the 2nd run of blast]
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122 File_OUT2.write("%s\n" %pair[2])
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123 seq_match = pair[3]
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124 seq_match_ungapped = string.replace(seq_match, "-", "")
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125 File_OUT2.write("%s\n" %seq_match_ungapped)
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126
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127 File_OUT.close()
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128 File_OUT2.close()