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Adding flag for large files to guidance.py

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Auden Cote-L'Heureux 2025-01-09 12:19:51 -05:00 committed by GitHub
parent 733851b957
commit 31a9295485
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1 changed files with 14 additions and 0 deletions
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PTL2/Scripts/guidance.py
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@ -53,6 +53,19 @@ def run(params):
guidance_removed_file = open(params.output + '/Output/GuidanceRemovedSeqs.txt', 'w') guidance_removed_file = open(params.output + '/Output/GuidanceRemovedSeqs.txt', 'w')
guidance_removed_file.write('Sequence\tScore\n') guidance_removed_file.write('Sequence\tScore\n')
too_many_seqs = False
#For each unaligned AA fasta file
for file in [f for f in os.listdir(guidance_input) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta')]:
nseqs = len([rec for rec in SeqIO.parse(guidance_input + '/' + file, 'fasta')])
if nseqs > 2000:
too_many_seqs = True
break
if too_many_seqs and not params.allow_large_files:
return False
#For each unaligned AA fasta file #For each unaligned AA fasta file
for file in [f for f in os.listdir(guidance_input) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta')]: for file in [f for f in os.listdir(guidance_input) if f.endswith('.fa') or f.endswith('.faa') or f.endswith('.fasta')]:
tax_guidance_outdir = params.output + '/Output/Intermediate/Guidance/Output/' + file.split('.')[0].split('_preguidance')[0] tax_guidance_outdir = params.output + '/Output/Intermediate/Guidance/Output/' + file.split('.')[0].split('_preguidance')[0]
@ -168,6 +181,7 @@ def run(params):
os.system('mv ' + tax_guidance_outdir + '/' + gdir_file + ' ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file) os.system('mv ' + tax_guidance_outdir + '/' + gdir_file + ' ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file)
guidance_removed_file.close() guidance_removed_file.close()
return True