[Bioperl-l] Genebank mRNAs

[Jason Stajich]

John -

Can you please submit example code and genbank accession numbers that cause
the behavior you describe in your bug reports.  It will greatly increase the
chances that someone will make the time to fix these bugs if we don't have
to spend time tracking down an example.  Ideally  we'd want to design a test
case for the bug in the t/SeqIO.t test file so we can properly test for it.
If you wanted to do this I know it will take one of us a lot less time to
fix it.

-Jason

----- Original Message -----
From: "Castle, John" <JCastle@rii.com>
To: <bioperl-l@bioperl.org>
Sent: Thursday, May 03, 2001 6:41 PM
Subject: [Bioperl-l] Genebank mRNAs


> Hi BioPerl,
>
> Thanks for the good perl scripts.  I'm having trouble with them and was
> wondering if someone could address this problem or refer me to someone
else.
>
> I'm trying to read in files in GenBank format and output the various mRNA
> sequences for each GenBank record.  Can I do this with the BioPerl
modules?
> (Side note - the SeqIO scripts choke on the headers contained in the NCBI
> Genbank flat files.)
>
> A given GenBank sequence may have several mRNAs, these "features" can be
> alternate splice forms and contain differing amounts of the total
sequence;
> this is specified by the "join" lines in the Genbank records.
>
> When I read in a Genbank file with subfeatures, I think the modules
> currently bless the subfeatures as Bio::SeqFeature::Generic objects.
> Unfortunately, when I ask for the sequence of a mRNA feature, it returns
the
> total sequence, not the mRNA sequence.
>
> Any ideas?
>
> Thanks,
> John Castle
>
>
>
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