[Biopython-dev] SeqIO circular

Matthias Bernt MatatTHC at gmx.de
Sat Apr 28 07:15:35 UTC 2012

Dear developers,

I would like to suggest a quick "fix" for the problem. Currently the
parser just returns true per default for the circular property. This
is a wrong piece of information for all circular sequences.
Furthermore its not possible to detect if the parser did return true
because it is its default value or if its really from the data. So I
suggest to return None if the parser does not parse the information.

What do you think? This should be possible with minimal effort.

The user could then implement a workaround on its own (like using the
old parser as fallback, or just searching the first line of t)


2012/4/22 Matthias Bernt <MatatTHC at gmx.de>:
> Hi,
> 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:
> http://search.cpan.org/~cjfields/BioPerl-1.6.1/Bio/Seq.pm
> http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/PrimarySeq.pm
> Or also:
> http://bugzilla.open-bio.org/show_bug.cgi?id=2578
> This seems to be realised as boolean variable or function.
> Regards,
> Matthias
> 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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