[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
Tue Jul 10 06:28:27 UTC 2012

Issue #3368 has been updated by Kai Blin.

Peter Cock wrote:
> 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 :(

No worries. In turn, I just learned that Redmine merges the Bugzilla fields "assignee" and "QA contact" into one field, and the "QA contact" meaning is the more important one for the way this project is run. :)

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

You mean integers instead of strings, I guess.  But yes, I can see the danger of breaking existing scripts, seeing how I even had to fix the "we only parse strings" assumption twice in the remaining parser code. I'm happy with the patch you pushed, thanks a lot.

Bug #3368: Bio.GenBank format writer creates invalid start_codon entries.

Author: Kai Blin
Status: Closed
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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