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althonos / pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
https://pyrodigal.readthedocs.org
GNU General Public License v3.0
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Error for contigs that do not contain coding regions using -p meta #44

Closed geronimp closed 9 months ago

geronimp commented 9 months ago

Hello,

Thanks for the great tool. When using pyrodigal v3.0.0 an error is thrown when a contig that does not contain a coding region is encountered. I came across this issue when using -p meta mode using the contig in the attached file.

pyrodigal -p meta -d outgene.fna -o outgene.gff -i blank_example.txt
Error: 'NoneType' object has no attribute 'description'

blank_example.txt

althonos commented 9 months ago

Hi @geronimp, thank you for your report. I have fixed the bug, which affected both Genes.write_gff and Genes.write_scores, and made a new patch release v3.0.1.

geronimp commented 9 months ago

Much appreciated, thank you!