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Halfway done with fix to wrapper.py

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Auden Cote-L'Heureux 2024-02-16 14:10:14 -05:00 committed by GitHub
parent 384dd72125
commit 93b328306a
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1 changed files with 1 additions and 1 deletions
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PTL1/Transcriptomes/Scripts/wrapper.py
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@ -149,7 +149,7 @@ def script_five(args):
lines = [line.strip().split('\t') for line in open(args.output + '/Output/gcode_output.tsv', 'r')]
with open(args.output + '/Output/gcode_output.tsv', 'r') as g:
for folder in os.listdir(args.output + '/Output'):
if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta'):
if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta') and os.path.isdir(args.output + '/Output/' + folder + '/StopCodonFreq'):
for line in lines:
if line[0] == folder and line[-1].lower() in valid_codes:
os.system('python 5_GCodeTranslate.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta --genetic_code ' + line[-1])