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oschwengers / bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
GNU General Public License v3.0
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Presumed GFF3/Gbff user regions file format error when replicon table is provided #326

Closed oschwengers closed 3 days ago

oschwengers commented 3 days ago

Bakta throws an error stating that the --regions-provided .gff3 / gbff file format is wrong when custom sequence IDs are provided via --replicons.

This is caused by https://github.com/oschwengers/bakta/blob/1e22eeb45f418cb162a7978623ab5d8994e6dc5f/bakta/utils.py#L463 copy a wrong seq id - actually not the original but the one generated in https://github.com/oschwengers/bakta/blob/1e22eeb45f418cb162a7978623ab5d8994e6dc5f/bakta/utils.py#L431.