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Fixing small oversight in concatenate.py

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Auden Cote-L'Heureux 2023-10-30 13:00:07 -04:00 committed by GitHub
parent 6f1c37bcbc
commit e90e177276
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1 changed files with 15 additions and 1 deletions
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PTL2/Scripts/concatenate.py
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@ -218,7 +218,21 @@ def concat(seqs_per_og, params):
taxa = list(dict.fromkeys([rec.id[:10] for og in seqs_per_og for rec in seqs_per_og[og]])) taxa = list(dict.fromkeys([rec.id[:10] for og in seqs_per_og for rec in seqs_per_og[og]]))
seqs_per_og = { og : { rec.id[:10] : str(rec.seq) for rec in seqs_per_og[og] } for og in seqs_per_og } seqs_per_og = { og : { rec.id : str(rec.seq).replace('-', '') for rec in seqs_per_og[og] } for og in seqs_per_og }
if not os.path.isdir(params.output + '/Output/DataToConcatenate'):
os.mkdir(params.output + '/Output/DataToConcatenate')
os.mkdir(params.output + '/Output/DataToConcatenate/Unaligned')
os.mkdir(params.output + '/Output/DataToConcatenate/Aligned')
for og in seqs_per_og:
with open(params.output + '/Output/DataToConcatenate/Unaligned/' + '.'.join(og.split('.')[:-1]) + '_TargetTaxaUnaligned.fasta', 'w') as o:
for tax in seqs_per_og[og]:
o.write('>' + tax + '\n' + seqs_per_og[og][tax] + '\n\n')
os.system('mafft ' + params.output + '/Output/DataToConcatenate/Unaligned/' + '.'.join(og.split('.')[:-1]) + '_TargetTaxaUnaligned.fasta > ' + params.output + '/Output/DataToConcatenate/Aligned/' + '.'.join(og.split('.')[:-1]) + '_TargetTaxaAligned.fasta')
seqs_per_og[og] = { rec.id[:10] : str(rec.seq) for rec in SeqIO.parse(params.output + '/Output/DataToConcatenate/Aligned/' + '.'.join(og.split('.')[:-1]) + '_TargetTaxaAligned.fasta', 'fasta') }
concat_seqs_per_tax = { tax : '' for tax in taxa } concat_seqs_per_tax = { tax : '' for tax in taxa }
for taxon in taxa: for taxon in taxa: