[Biopython] typo error “source_ersion” , it should be “source_version"

Peter Cock p.j.a.cock at googlemail.com
Sun Jan 26 13:18:47 UTC 2014


On Fri, Jan 24, 2014 at 1:50 PM, Alan <alanwilter at gmail.com> wrote:
> Hi Peter,
>
> I cannot promise, but I will try to see how to improve test_SeqIO_SeqXML.py.
> Meanwhile, another typo:
>
>         if self.species is not None:
>             if not isinstance(species, basestring):
>
> should be:
>
>         if self.species is not None:
>             if not isinstance(self.species, basestring):
>

Hi Alan,

That's fixed too now, thanks again:
https://github.com/biopython/biopython/commit/d06e85da15bae355219f1cfb767b93fb02d8130d

And I added a basic test which drew my attention to the fact that the
SeqXML parser was not fully compatible with the precedent set by
the plain text SwissProt and UniProt XML parsers (lists versus strings):
https://github.com/biopython/biopython/commit/91810c8acdd4d407b6820ef62cbf9fa591d9341d
https://github.com/biopython/biopython/commit/50f47b8a7e08be5e22f66be59f0eef23249d05e1

The SeqXML species stuff probably still needs more tests... in
particular chimeric records may cause trouble?

Regards,

Peter



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