[Biopython-dev] SeqXML an alternative for FASTA

[Peter Cock]

On Tue, Jul 5, 2011 at 5:10 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Hi all,
>
> I've been in touch with Thomas Schmitt about merging read/write
> support for the SeqXML file format (see below and http://seqxml.org/ )
> into Biopython's SeqIO module.
>
> BioPerl already supports this (under format name "seqxml") and a
> BioJava v3 implementation is in progress. We're discussing this and
> the format itself on the cross project OBF mailing list (see below),
>
> http://lists.open-bio.org/pipermail/open-bio-l/2011-July/000805.html
>
> Please feel free to join that list if you want to discuss anything
> general, or comment here on the Biopython implementation.
> I've got a branch which seems nearly ready for merging on
> github, https://github.com/peterjc/biopython/commits/seqxml2
> a rebase of https://github.com/peterjc/biopython/commits/seqxml
>
> Regards,
>
> Peter

I've just applied this to the trunk.

Thomas, please keep in touch if and when there are any further
changes to the seqxml specification and the code needs updating.

Thanks,

Peter