Mercurial > repos > dfornika > blast_report_basic

annotate blast_report.py @ 22:261235bbd475 draft

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author dfornika
date Tue, 03 Mar 2020 09:29:50 +0000
parents 9cf35f30bfb4
children 8d92b3b58f5e
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1 #!/usr/bin/env python
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3 from __future__ import print_function
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5 '''Report on BLAST results.
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7 python blast_report.py input_tab cheetah_tmpl output_html output_tab [-f [filter_pident]:[filterkw1,...,filterkwN]] [-b bin1_label=bin1_path[,...binN_label=binN_path]]
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8 '''
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10 import argparse
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11 import re
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12 import sys
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14 from Cheetah.Template import Template
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17 def stop_err( msg ):
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18 sys.stderr.write("%s\n" % msg)
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19 sys.exit(1)
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22 class BLASTBin:
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23 def __init__(self, label, file):
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24 self.label = label
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25 self.dict = {}
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27 file_in = open(file)
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28 for line in file_in:
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29 self.dict[line.rstrip().split('.')[0]] = ''
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30 file_in.close()
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32 def __str__(self):
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33 return "label: %s dict: %s" % (self.label, str(self.dict))
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36 class BLASTQuery:
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37 def __init__(self, query_id):
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38 self.query_id = query_id
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39 self.matches = []
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40 self.match_accessions = {}
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41 self.bins = {} #{bin(label):[match indexes]}
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42 self.pident_filtered = 0
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43 self.kw_filtered = 0
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44 self.kw_filtered_breakdown = {} #{kw:count}
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46 def __str__(self):
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47 return "query_id: %s len(matches): %s bins (labels only): %s pident_filtered: %s kw_filtered: %s kw_filtered_breakdown: %s" \
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48 % (self.query_id,
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49 str(len(self.matches)),
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50 str([bin.label for bin in bins]),
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51 str(self.pident_filtered),
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52 str(self.kw_filtered),
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53 str(self.kw_filtered_breakdown))
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56 class BLASTMatch:
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57 def __init__(self, subject_acc, subject_descr, score, p_cov, p_ident, subject_bins):
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58 self.subject_acc = subject_acc
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59 self.subject_descr = subject_descr
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60 self.score = score
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61 self.p_cov = p_cov
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62 self.p_ident = p_ident
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63 self.bins = subject_bins
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64
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65 def __str__(self):
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66 return "subject_acc: %s subject_descr: %s score: %s p-cov: %s p-ident: %s" \
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67 % (self.subject_acc,
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68 self.subject_descr,
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69 str(self.score),
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70 str(round(self.p_cov,2)),
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71 str(round(self.p_ident, 2)))
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74 #PARSE OPTIONS AND ARGUMENTS
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75 parser = argparse.ArgumentParser()
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76
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77 parser.add_argument('-f', '--filter-keywords',
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78 dest='filter_keywords',
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79 )
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80 parser.add_argument('-i', '--min-identity',
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81 dest='min_identity',
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82 )
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83 parser.add_argument('-b', '--bins',
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84 dest='bins'
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85 )
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86 parser.add_argument('-r', '--discard-redundant',
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87 dest='discard_redundant',
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88 default=False,
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89 action='store_true'
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90 )
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91 parser.add_argument('input_tab')
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92 parser.add_argument('cheetah_tmpl')
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93 parser.add_argument('output_html')
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94 parser.add_argument('output_tab')
0
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95 args = parser.parse_args()
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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96
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97 print('input_tab: %s cheetah_tmpl: %s output_html: %s output_tab: %s' % (args.input_tab, args.cheetah_tmpl, args.output_html, args.output_tab))
0
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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98
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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99
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
dfornika
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100 #BINS
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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101 bins=[]
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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102 if args.bins != None:
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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103 bins = list([BLASTBin(label_file.split('=')[0],label_file.split('=')[-1]) for label_file in args.bins.split(',')])
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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104 print('database bins: %s' % str([bin.label for bin in bins]))
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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105
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106 #FILTERS
0
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107 filter_pident = 0
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108 filter_kws = []
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109 if args.filter_keywords:
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110 filter_kws = args.filter_keywords.split(',')
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111 print('minimum percent identity: %s filter_kws: %s' % (str(args.min_identity), str(filter_kws)))
0
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112
3
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113 if args.discard_redundant:
0
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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114 print('Throwing out redundant hits...')
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115
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116
0
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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117 PIDENT_COL = 2
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118 DESCR_COL = 24
0
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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119 SUBJ_ID_COL = 12
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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120 SCORE_COL = 11
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121 PCOV_COL = 25
0
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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122 queries = []
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123 current_query = ''
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124 output_tab = open(args.output_tab, 'w')
0
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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125
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126 with open(args.input_tab) as input_tab:
0
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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127 for line in input_tab:
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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128 cols = line.split('\t')
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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129 if cols[0] != current_query:
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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130 current_query = cols[0]
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131 queries.append(BLASTQuery(current_query))
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132
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133 try:
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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134 accs = cols[SUBJ_ID_COL].split('|')[1::2][1::2]
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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135 except IndexError as e:
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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136 stop_err("Problem with splitting:" + cols[SUBJ_ID_COL])
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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137
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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138 #hsp option: keep best (first) hit only for each query and accession id.
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139 if args.discard_redundant:
0
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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140 if accs[0] in queries[-1].match_accessions:
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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141 continue #don't save the result and skip to the next
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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142 else:
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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143 queries[-1].match_accessions[accs[0]] = ''
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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144
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145
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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146 p_ident = float(cols[PIDENT_COL])
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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147 #FILTER BY PIDENT
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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148 if p_ident < filter_pident: #if we are not filtering, filter_pident == 0 and this will never evaluate to True
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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149 queries[-1].pident_filtered += 1
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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150 continue
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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151
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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152 descrs = cols[DESCR_COL]
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153 #FILTER BY KEY WORDS
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154 filter_by_kw = False
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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155 for kw in filter_kws:
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156 kw = kw.strip()
0
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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157 if kw != '' and re.search(kw, descrs, re.IGNORECASE):
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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158 filter_by_kw = True
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159 try:
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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160 queries[-1].kw_filtered_breakdown[kw] += 1
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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161 except:
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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162 queries[-1].kw_filtered_breakdown[kw] = 1
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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163 if filter_by_kw: #if we are not filtering, for loop will not be entered and this will never be True
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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164 queries[-1].kw_filtered += 1
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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165 continue
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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166 descr = descrs.split(';')[0]
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167
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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168 #ATTEMPT BIN
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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169 subj_bins = []
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170 for bin in bins: #if we are not binning, bins = [] so for loop not entered
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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171 for acc in accs:
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172 if acc.split('.')[0] in bin.dict:
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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173 try:
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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174 queries[-1].bins[bin.label].append(len(queries[-1].matches))
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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175 except:
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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176 queries[-1].bins[bin.label] = [len(queries[-1].matches)]
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177 subj_bins.append(bin.label)
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178 break #this result has been binned to this bin so break
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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179 acc = accs[0]
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180
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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181 score = int(float(cols[SCORE_COL]))
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182 p_cov = float(cols[PCOV_COL])
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183
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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184 #SAVE RESULT
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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185 queries[-1].matches.append(
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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186 BLASTMatch(acc, descr, score, p_cov, p_ident, subj_bins)
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187 )
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188 output_tab.write(line)
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189 input_tab.close()
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190 output_tab.close()
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191
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192 '''
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193 for query in queries:
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194 print(query)
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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195 for match in query.matches:
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196 print(' %s' % str(match))
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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197 for bin in query.bins:
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198 print(' bin: %s' % bin)
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199 for x in query.bins[bin]:
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200 print(' %s' % str(query.matches[x]))
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201 '''
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202
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203 namespace = {'queries': queries}
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204 html = Template(file=args.cheetah_tmpl, searchList=[namespace])
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205 out_html = open(args.output_html, 'w')
0
5dfd84907521 planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
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206 out_html.write(str(html))
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207 out_html.close()
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208