Mercurial > repos > dfornika > blast_report_basic

comparison blast_report.py @ 0:5dfd84907521 draft

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planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
author dfornika
date Tue, 03 Mar 2020 00:14:34 +0000
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children 386a88793078
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-1:000000000000 0:5dfd84907521
1 #!/usr/bin/env python
2 '''Report on BLAST results.
3
4 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]]
5 '''
6 import argparse
7 import re
8 import sys
9
10 from Cheetah.Template import Template
11
12
13 def stop_err( msg ):
14 sys.stderr.write("%s\n" % msg)
15 sys.exit(1)
16
17
18 class BLASTBin:
19 def __init__(self, label, file):
20 self.label = label
21 self.dict = {}
22
23 file_in = open(file)
24 for line in file_in:
25 self.dict[line.rstrip().split('.')[0]] = ''
26 file_in.close()
27
28 def __str__(self):
29 return "label: %s dict: %s" % (self.label, str(self.dict))
30
31
32 class BLASTQuery:
33 def __init__(self, query_id):
34 self.query_id = query_id
35 self.matches = []
36 self.match_accessions = {}
37 self.bins = {} #{bin(label):[match indexes]}
38 self.pident_filtered = 0
39 self.kw_filtered = 0
40 self.kw_filtered_breakdown = {} #{kw:count}
41
42 def __str__(self):
43 return "query_id: %s len(matches): %s bins (labels only): %s pident_filtered: %s kw_filtered: %s kw_filtered_breakdown: %s" \
44 % (self.query_id,
45 str(len(self.matches)),
46 str([bin.label for bin in bins]),
47 str(self.pident_filtered),
48 str(self.kw_filtered),
49 str(self.kw_filtered_breakdown))
50
51
52 class BLASTMatch:
53 def __init__(self, subject_acc, subject_descr, score, p_cov, p_ident, subject_bins):
54 self.subject_acc = subject_acc
55 self.subject_descr = subject_descr
56 self.score = score
57 self.p_cov = p_cov
58 self.p_ident = p_ident
59 self.bins = subject_bins
60
61 def __str__(self):
62 return "subject_acc: %s subject_descr: %s score: %s p-cov: %s p-ident: %s" \
63 % (self.subject_acc,
64 self.subject_descr,
65 str(self.score),
66 str(round(self.p_cov,2)),
67 str(round(self.p_ident, 2)))
68
69
70
71 #PARSE OPTIONS AND ARGUMENTS
72 parser = argparse.ArgumentParser()
73
74 parser.add_argument('-f', '--filter',
75 type='string',
76 dest='filter',
77 )
78 parser.add_argument('-b', '--bins',
79 type='string',
80 dest='bins'
81 )
82 parser.add_argument('-r', '--redundant',
83 dest='redundant',
84 default=False,
85 action='store_true'
86 )
87 args = parser.parse_args()
88
89 try:
90 input_tab, cheetah_tmpl, output_html, output_tab = args
91 except:
92 stop_err('you must supply the arguments input_tab, cheetah_tmpl and output_html.')
93 # print('input_tab: %s cheetah_tmpl: %s output_html: %s output_tab: %s' % (input_tab, cheetah_tmpl, output_html, output_tab))
94
95
96 #BINS
97 bins=[]
98 if args.bins != None:
99 bins = list([BLASTBin(label_file.split('=')[0],label_file.split('=')[-1]) for label_file in args.bins.split(',')])
100 print('database bins: %s' % str([bin.label for bin in bins]))
101
102 #FILTERS
103 filter_pident = 0
104 filter_kws = []
105 if args.filter != None:
106 pident_kws = args.filter.split(':')
107 filter_pident = float(pident_kws[0])
108 filter_kws = pident_kws[-1].split(',')
109 print('filter_pident: %s filter_kws: %s' % (str(filter_pident), str(filter_kws)))
110
111 if args.redundant:
112 print('Throwing out redundant hits...')
113
114 #RESULTS!
115 PIDENT_COL = 2
116 DESCR_COL = 25
117 SUBJ_ID_COL = 12
118 SCORE_COL = 11
119 PCOV_COL = 24
120 queries = []
121 current_query = ''
122 output_tab = open(output_tab, 'w')
123
124 with open(input_tab) as input_tab:
125 for line in input_tab:
126 cols = line.split('\t')
127 if cols[0] != current_query:
128 current_query = cols[0]
129 queries.append(BLASTQuery(current_query))
130
131 try:
132 accs = cols[SUBJ_ID_COL].split('|')[1::2][1::2]
133 except IndexError as e:
134 stop_err("Problem with splitting:" + cols[SUBJ_ID_COL])
135
136 #hsp option: keep best (first) hit only for each query and accession id.
137 if args.redundant:
138 if accs[0] in queries[-1].match_accessions:
139 continue #don't save the result and skip to the next
140 else:
141 queries[-1].match_accessions[accs[0]] = ''
142
143
144 p_ident = float(cols[PIDENT_COL])
145 #FILTER BY PIDENT
146 if p_ident < filter_pident: #if we are not filtering, filter_pident == 0 and this will never evaluate to True
147 queries[-1].pident_filtered += 1
148 continue
149
150 descrs = cols[DESCR_COL]
151 #FILTER BY KEY WORDS
152 filter_by_kw = False
153 for kw in filter_kws:
154 kw = kw.strip() #Fix by Damion D Nov 2013
155 if kw != '' and re.search(kw, descrs, re.IGNORECASE):
156 filter_by_kw = True
157 try:
158 queries[-1].kw_filtered_breakdown[kw] += 1
159 except:
160 queries[-1].kw_filtered_breakdown[kw] = 1
161 if filter_by_kw: #if we are not filtering, for loop will not be entered and this will never be True
162 queries[-1].kw_filtered += 1
163 continue
164 descr = descrs.split(';')[0]
165
166 #ATTEMPT BIN
167 subj_bins = []
168 for bin in bins: #if we are not binning, bins = [] so for loop not entered
169 for acc in accs:
170 if acc.split('.')[0] in bin.dict:
171 try:
172 queries[-1].bins[bin.label].append(len(queries[-1].matches))
173 except:
174 queries[-1].bins[bin.label] = [len(queries[-1].matches)]
175 subj_bins.append(bin.label)
176 break #this result has been binned to this bin so break
177 acc = accs[0]
178
179 score = int(float(cols[SCORE_COL]))
180 p_cov = float(cols[PCOV_COL])
181
182 #SAVE RESULT
183 queries[-1].matches.append(
184 BLASTMatch(acc, descr, score, p_cov, p_ident, subj_bins)
185 )
186 output_tab.write(line)
187 input_tab.close()
188 output_tab.close()
189
190 '''
191 for query in queries:
192 print(query)
193 for match in query.matches:
194 print(' %s' % str(match))
195 for bin in query.bins:
196 print(' bin: %s' % bin)
197 for x in query.bins[bin]:
198 print(' %s' % str(query.matches[x]))
199 '''
200
201 namespace = {'queries': queries}
202 html = Template(file=cheetah_tmpl, searchList=[namespace])
203 out_html = open(output_html, 'w')
204 out_html.write(str(html))
205 out_html.close()
206
207
208 if __name__ == '__main__':
209 main()