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Fix broken code in pyrodigal.cli
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althonos committed Jul 17, 2024
1 parent 62fc60c commit f4c56f3
Showing 1 changed file with 6 additions and 6 deletions.
12 changes: 6 additions & 6 deletions pyrodigal/cli.py
Original file line number Diff line number Diff line change
Expand Up @@ -296,21 +296,21 @@ def main(

# process sequence in parallel if possible
process = functools.partial(_process, gene_finder)
for seq, preds in parallel_map(process, sequences):
for seq_id, preds in parallel_map(process, sequences):
# write output in GFF or GBK format
if args.f == "gff":
preds.write_gff(out_file, seq.id)
preds.write_gff(out_file, seq_id)
elif args.f == "gbk":
preds.write_genbank(out_file, seq.id)
preds.write_genbank(out_file, seq_id)
# if asked, write nucleotide sequences of genes
if nuc_file is not None:
preds.write_genes(nuc_file, seq.id)
preds.write_genes(nuc_file, seq_id)
# if asked, write amino acid sequences of proteins
if prot_file is not None:
preds.write_translations(prot_file, seq.id, include_stop=args.no_stop_codon)
preds.write_translations(prot_file, seq_id, include_stop=args.no_stop_codon)
# if asked, write scores
if scores_file is not None:
preds.write_scores(scores_file, seq.id)
preds.write_scores(scores_file, seq_id)

except Exception as err:
print("Error: {}".format(err))
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