[Biopython-dev] SeqIO circular

Matthias Bernt MatatTHC at gmx.de
Wed Apr 4 08:46:47 UTC 2012


are there any news on this? May I help somehow? But I have to admit
that I barely speak perl and have no experience with bioperl. If
someone tells me where to look I might still try it.


2012/3/29 Peter Cock <p.j.a.cock at googlemail.com>:
> On Thu, Mar 29, 2012 at 3:38 PM, Matthias Bernt <MatatTHC at gmx.de> wrote:
>> Hi,
>> Is it possible to get the property if a genome is circular / linear
>> from SeqIO applied to genbank files? I could not find it.
>> There is also a related bugreport:
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2578
>> I used the old parser before and switched to SeqIO which I really like
>> for the possibilities to parse different formats... but I really need
>> the information.
> Does anyone happen to have a BioPerl + BioSQL setup installed
> and working? IIRC checking that to make sure however we
> store the circular was compatible was the only real hurdle.
> Peter

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