Mercurial > repos > dfornika > micall_lite

comparison amino2consensus.py @ 22:b5df889acab3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/micall-lite commit 822e7e1c2de31a72c2a13bcc15b9df06b699561f-dirty
author dfornika
date Wed, 25 Sep 2019 19:08:16 -0400
parents d099ef46fd42
children 033e0a3674bc
comparison
equal deleted inserted replaced
21:d099ef46fd42 22:b5df889acab3
8 AMINO_ACIDS = ['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y','*'] 8 AMINO_ACIDS = ['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y','*']
9 9
10 def determine_amino(amino_counts, threshold): 10 def determine_amino(amino_counts, threshold):
11 amino = "" 11 amino = ""
12 total_count = sum(amino_counts.values()) 12 total_count = sum(amino_counts.values())
13 amino_with_max_counts, count = sorted(amino_counts.items(), key=lambda item: item[1], reverse=True)[0] 13 amino_with_max_counts = sorted(amino_counts, key=amino_counts.get, reverse=True)[0]
14 if total_count == 0: 14 if total_count == 0:
15 amino = "#" 15 amino = "#"
16 elif (amino_counts[amino_with_max_counts] / float(total_count)) > threshold: 16 elif (amino_counts[amino_with_max_counts] / float(total_count)) > threshold:
17 amino = amino_with_max_counts 17 amino = amino_with_max_counts
18 else: 18 else:
53 53
54 54
55 if __name__ == '__main__': 55 if __name__ == '__main__':
56 parser = argparse.ArgumentParser() 56 parser = argparse.ArgumentParser()
57 parser.add_argument("amino", help="MiCall amino.csv output file") 57 parser.add_argument("amino", help="MiCall amino.csv output file")
58 parser.add_argument("--threshold", default=0.15, help="Threshold for calling") 58 parser.add_argument("--threshold", default=0.15, type=float, help="Threshold for calling")
59 args = parser.parse_args() 59 args = parser.parse_args()
60 main(args) 60 main(args)