Re: User-defined annotations in Stockholm alignment file
Peter Cock <[email protected]>
| Newsgroups | gmane.comp.python.bio.devel |
|---|---|
| Message-ID | <CAKVJ-_6eoJd=w0DxmuGv_pz=8FJv+-HYkd6+GNTjb1ym2zxuDQ@mail.gmail.com> |
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 < [email protected]> 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? > > _______________________________________________ Biopython-dev mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/biopython-dev