[Bioperl-l] bp_genbank2gff3.pl error on last line ("//")

Chris Fields cjfields at illinois.edu
Sun Jul 25 19:11:06 EDT 2010


On Jul 25, 2010, at 4:10 PM, Peter wrote:

> On Sun, Jul 25, 2010 at 8:52 PM, David Breimann
> <david.breimann at gmail.com> wrote:
>> Thank you guys. I'm quite new to all this github stuff, so in order to view
>> to use to updated version should I first update my clone of bioperl-live
>> (git pull?) then go through the whole build and install again?
>> 
>> Second, I have just noticed that bp_genbank2gff3.pl returns an error when
>> given a circular genome with a feature that spans the "end" of the genome
>> (e.g., assume the genome size is 1000np and a feature spans
>> join(900..1000,1..100).
> 
> The GFF3 spec has recently been updated to cover circular
> genomes explicitly - this script probably needs updating in light
> of this.
> 
> Peter

We need to add a few tests for circular genomes with BioPerl; I'm pretty sure these currently do not work as expected.

chris




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