[Biopython-dev] [Biopython - Bug #3368] Bio.GenBank format writer creates invalid start_codon entries.

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Mon Jul 9 22:40:18 UTC 2012

Issue #3368 has been updated by Peter Cock.

Assignee changed from Kai Blin to Biopython Dev Mailing List

Apologies for apparently ignoring you - I've just changed the assignee (back to) Biopython Dev Mailing List, since no-one was getting any of these updates by email. Well, I wasn't at least :(

I'm wary about changing the parser to give integers instead of ints - that seems likely to break existing scripts.

The whitelist approach in https://github.com/kblin/biopython/commit/4dec86810a42743967981b74c81a6fb8e17004e4 seems a better bet.
Bug #3368: Bio.GenBank format writer creates invalid start_codon entries.

Author: Kai Blin
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 
URL: ftp://ftp.ncbi.nih.gov/genbank/release.notes/gb185.release.notes

When writing genbank output, the module adds quotes around the codon_start qualifier. This isn't according to the genbank file spec (see URL), and it also breaks the parser of another program I need to use.

BioPython generates:
while it should generate:

Looking over the Bio.GenBank code, it seems like I need to introduce some special handling for un-quoted qualifiers. I'd suggest using the same list as BioPerl:


our %FTQUAL_NO_QUOTE = map {$_ => 1} qw(
    anticodon           citation
    codon               codon_start
    cons_splice         direction
    evidence            label
    mod_base            number
    rpt_type            rpt_unit
    transl_except       transl_table
</pre> (see https://github.com/bioperl/bioperl-live/blob/master/Bio/SeqIO/genbank.pm#L193)

I'll try to come up with a patch and will be happy for feedback on implementation, coding conventions and the like.

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