[Biopython-dev] SeqXML an alternative for FASTA

Peter Cock p.j.a.cock at googlemail.com
Thu Jul 14 13:15:12 UTC 2011

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.



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