[Biopython] Status of GFF3 parser in BioPython?

[Peter Cock]

Hi Bastien,

I think this is really dependent on Brad (as the GFF3 parser
author) and/or me (as the SeqIO owner and thus defacto
owner of the SeqRecord, SeqFeature etc objects) to make
time for this. Or a keen third party volunteer might make it
happen?

Unfortunately I can't promise anything right now, but
recently I have been doing more work with annotation,
so this might be possible on work time - like my recent
contributions to the Sanger Pathogen group's tool for
turning Prokka GFF into ENA ready EMBL files:
https://github.com/sanger-pathogens/gff3toembl

Right now depending on both Biopython and Brad's
GFF library might be reasonable - both are on PyPI:

https://pypi.python.org/pypi/biopython
https://pypi.python.org/pypi/bcbio-gff

Peter

On Wed, Nov 16, 2016 at 3:50 PM, Chevreux, Bastien
<bastien.chevreux at dsm.com> wrote:
> Hi there,
>
>
>
> I am wondering about the status of a GFF3 parser in BioPython. According to
> the BioPython website it is in development and not integrated yet. If I read
> an entry on BioStars right (https://www.biostars.org/p/2492/), it is like
> that since at least 6 years. Any news on that?
>
>
>
> Background: I am writing a script intended for wider publication, and while
> I can reasonably expect BioPython to be installed on many current platforms,
> I want to keep the number of non-standard dependencies low so as not to have
> unnecessary hurdles for untrained users.
>
>
>
> Best,
>
>   Bastien
>
>
>
> --
> DSM Nutritional Products Microbia Inc | Bioinformatics
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>
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