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

João Rodrigues j.p.g.l.m.rodrigues at gmail.com
Tue Apr 5 16:57:54 UTC 2016

Yeah, that's basically it... For both statements.

Regardless, about the custom annotations, should I give it a try and get it
to work? My plan was to have whatever is mapped to a pfam or rfam key
extended, as is now, and whatever else just kept under the two-character

A ter, 5/04/2016, 09:41, Peter Cock <p.j.a.cock at googlemail.com> escreveu:

> 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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