[Bioperl-l] bp_genbank2gff3.pl error with circular genomes
cjfields at illinois.edu
Tue Aug 17 15:24:23 EDT 2010
On Aug 17, 2010, at 10:53 AM, Chris Mungall wrote:
> You can merge this in. It should allow David to proceed.
Will do. I'll go ahead and delete the remote branch as well.
> I haven't kept up on synchrony between bioperl and GFF on circular genomes. The above fix is conservative in that essentially preserves the genbank coordinates even when the origin is crossed:
> However, if this is to conform to GFF3 then the resulting coordinates that cross the origin should have start/end incremented by the genome length
Yes, that is a problem that needs to be addressed. Might be worth filing a bug report for tracking this; we can use David's example, or the one I recently added for phi-X174.
> On Aug 17, 2010, at 6:51 AM, Chris Fields wrote:
>> I think Chris Mungall has a branch set up for this in bioperl:
>> Is that correct? Should we merge that code into the master branch?
>> On Aug 17, 2010, at 8:44 AM, David Breimann wrote:
>>> The following genbank has a gene that runs over the 'end" of the
>>> chromosome and into its "beginning", and the script generates an
>>> NC_005707 Unflattening error:
>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>> MSG: PROBLEM, SEVERITY==2
>>> Ranges not in correct order. Strange ensembl genbank entry? Range:
>>> [207497,208369] [1,687]
>>> STACK: Error::throw
>>> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:473
>>> STACK: Bio::SeqFeature::Tools::Unflattener::problem
>>> STACK: Bio::SeqFeature::Tools::Unflattener::_check_order_is_consistent
>>> STACK: Bio::SeqFeature::Tools::Unflattener::infer_mRNA_from_CDS
>>> STACK: Bio::SeqFeature::Tools::Unflattener::unflatten_seq
>>> STACK: main::unflatten_seq /usr/local/bin/bp_genbank2gff3.pl:1023
>>> STACK: /usr/local/bin/bp_genbank2gff3.pl:506
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
More information about the Bioperl-l