[Biopython] LOCUS name length on GenBank output: option to adjust?

[Chevreux, Bastien]

Dear list,

could BioPython implement an option to adjust the strictness of name length checking of a sequence when writing GenBank output?

I am aware of the short discussion in
  https://github.com/biopython/biopython/issues/526

and that BioPython wants to be strict on writing GenBank. However, I beg to reconsider this decision and allow for a user override.

Background: annotation of metagenomics / metatranscriptomic datasets where one can easily have a million contigs or more. Projects were named accordingly short so that names of DNA sequences fit into 16 characters. However, what was not considered was GenBank output of peptides, where the locus names are <name_of_contig>+<underscore>+<CDScounter_in_contig> ... and that may go up to 20.

As we are talking protein sequences here and there is no known protein >99999 amino acids, there would be a lot of wiggle room to allow the user to set a 20 char limit (or more) during GB output.

Best,
  Bastien

--
DSM Nutritional Products Microbia Inc | Bioinformatics
60 Westview Street | Lexington, MA 02421 | United States
Phone +1 781 259 7613 | Fax +1 781 259 0615


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