[Biopython-dev] SeqIO circular

Matthias Bernt MatatTHC at gmx.de
Sun Apr 22 10:06:28 UTC 2012


since this bug seems to be of low priority I decided to try my best to
help a bit and search the web a bit.
It seems that the property is stored in PrimarySeq or Seq  in bioperl.
See for instance:


Or also:

This seems to be realised as boolean variable or function.


2012/4/4 Matthias Bernt <MatatTHC at gmx.de>:
> Hi,
> 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.
> Matthias
> 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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