Parsing HMMER3 files

[multimeric]

Hi,

I'm interested in using this library for visualisation. However, something missing from this library that sounds useful to me is the ability to parse model files, as in practise this is how the probabilities are stored. Is there any way to convert from .hmm file -> hmm class instance? The .hmm format I'm interesting is the one used by the hmmer3 tool, which is described in section 8 of the hmmer user guide: http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf.

If you don't know of a method for doing this, would you accept a PR for this? My question is then whether specific bioinformatics formats are within scope for this package.

[helske]

I'm not familiar with hmmer3 format, but I don't see why this (or other) formats couldn't be supported if you think the package would be useful for analysing such models. So yes, I'll gladly accept PR especially if it includes a small example case.

[multimeric]

It's a format used by hmmer which is used for bioinformatics sequence classification (gene, proteins etc). But if you're okay with a specific bioinformatics format being included then I'll think about writing a parser for it.