Mercurial > repos > earlhaminst > blast_parser

comparison blast_parser.py @ 3:70df762b48a8 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/blast_parser commit 32272744ad83a704fd427b48aae574496a279901-dirty
author earlhaminst
date Tue, 03 Oct 2017 04:51:45 -0400
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children 363f3480622d
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2:376ed15e0d27 3:70df762b48a8
1 """
2 Simple parser to convert a BLAST 12-column or 24-column tabular output into a
3 3-column tabular input for hcluster_hg (id1, id2, weight):
4 """
5 import argparse
6 import math
7 from collections import OrderedDict
8
9
10 def main():
11 parser = argparse.ArgumentParser()
12
13 parser.add_argument('-i', metavar='in-file', type=argparse.FileType('rt'), required=True, help='Path to input file')
14
15 parser.add_argument('-o', metavar='out-file', type=argparse.FileType('wt'), required=True, help='Path to output file')
16
17 parser.add_argument('-r', action='store_true', default=False,
18 dest='reciprocal',
19 help='Annotate homolog pair')
20
21 parser.add_argument('--version', action='version', version='%(prog)s 1.0')
22
23 options = parser.parse_args()
24
25 results = OrderedDict()
26
27 for line in options.i:
28 line = line.rstrip()
29 line_cols = line.split('\t')
30 sequence1_id = line_cols[0]
31 sequence2_id = line_cols[1]
32 evalue = float(line_cols[10])
33
34 # Ignore self-matching hits
35 if sequence1_id != sequence2_id:
36 # Convert evalue to an integer weight with max 100
37 weight = 100
38
39 # If the evalue is 0, leave weight at 100
40 if evalue != 0.0:
41 weight = min(100, round(math.log10(evalue) / -2.0))
42
43 if (sequence1_id, sequence2_id) not in results:
44 results[(sequence1_id, sequence2_id)] = weight
45 else:
46 results[(sequence1_id, sequence2_id)] = max(results[(sequence1_id, sequence2_id)], weight)
47
48 for (sequence1_id, sequence2_id), weight in results.items():
49 if not options.reciprocal or (sequence2_id, sequence1_id) in results:
50 options.o.write("%s\t%s\t%d\n" % (sequence1_id, sequence2_id, weight))
51
52
53 if __name__ == "__main__":
54 main()