Mercurial > repos > dfornika > micall_lite

comparison amino2consensus.py @ 23:033e0a3674bc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit d5fd8bc70d31d99c2354f1e8ec2e34d147cfa048-dirty"
author dfornika
date Mon, 06 Jan 2020 23:49:32 +0000
parents b5df889acab3
children
comparison
equal deleted inserted replaced
22:b5df889acab3 23:033e0a3674bc
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 2
3 from __future__ import print_function 3 from __future__ import print_function
4 4
5 import argparse
5 import csv 6 import csv
6 import argparse
7 7
8 AMINO_ACIDS = ['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y','*'] 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
9 11
10 def determine_amino(amino_counts, threshold): 12 def determine_amino(amino_counts, threshold):
11 amino = "" 13 amino = ""
12 total_count = sum(amino_counts.values()) 14 total_count = sum(amino_counts.values())
13 amino_with_max_counts = sorted(amino_counts, key=amino_counts.get, reverse=True)[0] 15 amino_with_max_counts = sorted(amino_counts, key=amino_counts.get, reverse=True)[0]
17 amino = amino_with_max_counts 19 amino = amino_with_max_counts
18 else: 20 else:
19 amino = "@" 21 amino = "@"
20 return amino 22 return amino
21 23
24
22 def determine_first_region(amino_file): 25 def determine_first_region(amino_file):
23 with open(amino_file) as f: 26 with open(amino_file) as f:
24 reader = csv.DictReader(f) 27 reader = csv.DictReader(f)
25 row = next(reader) 28 row = next(reader)
26 region = row['region'] 29 region = row['region']
27 return region 30 return region
31
28 32
29 def main(args): 33 def main(args):
30 current_region = determine_first_region(args.amino) 34 current_region = determine_first_region(args.amino)
31 seq = [] 35 seq = []
32 with open(args.amino) as f: 36 with open(args.amino) as f:
48 amino_counts[amino_acid] = int(row[amino_acid]) 52 amino_counts[amino_acid] = int(row[amino_acid])
49 amino = determine_amino(amino_counts, args.threshold) 53 amino = determine_amino(amino_counts, args.threshold)
50 seq.append(amino) 54 seq.append(amino)
51 print(">" + current_region) 55 print(">" + current_region)
52 print(''.join(seq)) 56 print(''.join(seq))
53 57
54 58
55 if __name__ == '__main__': 59 if __name__ == '__main__':
56 parser = argparse.ArgumentParser() 60 parser = argparse.ArgumentParser()
57 parser.add_argument("amino", help="MiCall amino.csv output file") 61 parser.add_argument("amino", help="MiCall amino.csv output file")
58 parser.add_argument("--threshold", default=0.15, type=float, help="Threshold for calling") 62 parser.add_argument("--threshold", default=0.15, type=float, help="Threshold for calling")
59 args = parser.parse_args() 63 args = parser.parse_args()