Mercurial > repos > dfornika > micall_lite
diff amino2consensus.py @ 23:033e0a3674bc draft
"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 |
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--- a/amino2consensus.py Wed Sep 25 19:08:16 2019 -0400 +++ b/amino2consensus.py Mon Jan 06 23:49:32 2020 +0000 @@ -2,10 +2,12 @@ from __future__ import print_function +import argparse import csv -import argparse + -AMINO_ACIDS = ['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y','*'] +AMINO_ACIDS = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y', '*'] + def determine_amino(amino_counts, threshold): amino = "" @@ -19,6 +21,7 @@ amino = "@" return amino + def determine_first_region(amino_file): with open(amino_file) as f: reader = csv.DictReader(f) @@ -26,6 +29,7 @@ region = row['region'] return region + def main(args): current_region = determine_first_region(args.amino) seq = [] @@ -50,8 +54,8 @@ seq.append(amino) print(">" + current_region) print(''.join(seq)) - - + + if __name__ == '__main__': parser = argparse.ArgumentParser() parser.add_argument("amino", help="MiCall amino.csv output file")