[Biopython-dev] User-defined annotations in Stockholm alignment file

[Peter Cock]

If we agree with the hmmer treatment of this text as a description, then
everything
is working as designed? Not ideal, but over-interpreting free text isn't
either.

I wonder if hmmer could do something smarter with the FASTA input - but
that's
not up to us.

Peter

On Tue, Apr 5, 2016 at 5:21 PM, João Rodrigues <
j.p.g.l.m.rodrigues at gmail.com> wrote:

> Got in touch with Sean Eddy and apparently the issue is that hmmer reads
> the info from the original database file, which is in FASTA format, and
> then considers it as description. There's no attempt to parse any of that
> info because of the lack of semantics in FASTA headers.
>
> I'd be in favor of adding a sub parser for this info,  although I'm not
> sure how popular it would be. Making it separate from the main Stockholm
> parser makes sense for me, this is a special case. What do you think?
>
>
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