add ORGANISM label to GBK output

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

132 stars 5 forks source link

add ORGANISM label to GBK output #45

Open GeoMicroSoares opened 9 months ago

GeoMicroSoares commented 9 months ago

Hi there @althonos , Thanks so much for your work on this tool, it's just great! I'm using pyrodigal to generate GBK files from some MAGs I curated that I want to use as input for zDB (https://github.com/metagenlab/zDB/tree/d9069abbc92e60236a5fbe645ed1030ca6eaab2c), and noticed that tool checks the ORGANISM section of input GBK files (https://github.com/search?q=repo%3Ametagenlab%2FzDB+sci_name&type=code). Would it be possible to include a flag for this in pyrodigal? Thanks in advance!

althonos commented 7 months ago

HI @GeoMicroSoares,

To be honest I'm a bit reluctant to add support for this, because the GenBank writer is in a very crude form. I try supporting GenBank output for convenience but I don't want to implement a fully fledged GenBank writer, or have to depend on one, to support the different use cases when it's not the core of the library. I would recommend that you either use the API in combination with Biopython to write a GenBank file that contains the metadata you need.