Mercurial > repos > public-health-bioinformatics > micall_lite

comparison amino2consensus.py @ 0:023064145bea draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
author public-health-bioinformatics
date Mon, 06 Jan 2020 19:10:15 -0500
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-1:000000000000 0:023064145bea
1 #!/usr/bin/env python
2
3 from __future__ import print_function
4
5 import argparse
6 import csv
7
8
9 AMINO_ACIDS = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y', '*']
10
11
12 def determine_amino(amino_counts, threshold):
13 amino = ""
14 total_count = sum(amino_counts.values())
15 amino_with_max_counts = sorted(amino_counts, key=amino_counts.get, reverse=True)[0]
16 if total_count == 0:
17 amino = "#"
18 elif (amino_counts[amino_with_max_counts] / float(total_count)) > threshold:
19 amino = amino_with_max_counts
20 else:
21 amino = "@"
22 return amino
23
24
25 def determine_first_region(amino_file):
26 with open(amino_file) as f:
27 reader = csv.DictReader(f)
28 row = next(reader)
29 region = row['region']
30 return region
31
32
33 def main(args):
34 current_region = determine_first_region(args.amino)
35 seq = []
36 with open(args.amino) as f:
37 reader = csv.DictReader(f)
38 for row in reader:
39 if row['region'] == current_region:
40 amino_counts = {}
41 for amino_acid in AMINO_ACIDS:
42 amino_counts[amino_acid] = int(row[amino_acid])
43 amino = determine_amino(amino_counts, args.threshold)
44 seq.append(amino)
45 else:
46 print(">" + current_region)
47 print(''.join(seq))
48 current_region = row['region']
49 seq = []
50 amino_counts = {}
51 for amino_acid in AMINO_ACIDS:
52 amino_counts[amino_acid] = int(row[amino_acid])
53 amino = determine_amino(amino_counts, args.threshold)
54 seq.append(amino)
55 print(">" + current_region)
56 print(''.join(seq))
57
58
59 if __name__ == '__main__':
60 parser = argparse.ArgumentParser()
61 parser.add_argument("amino", help="MiCall amino.csv output file")
62 parser.add_argument("--threshold", default=0.15, type=float, help="Threshold for calling")
63 args = parser.parse_args()
64 main(args)