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

[João Rodrigues]

>
> Talk to the HMMER team first. If they have good reason and a citable
> authority for this file format change, we could support it directly?
>

Will do.


>
> > My original question was why does AlignIO ignore "custom" annotations it
> > doesn't know, while writing (StockholmIO, line 254)?
>
>
> https://github.com/biopython/biopython/blob/master/Bio/AlignIO/StockholmIO.py#L254
>
> Because as far as I know only a short list of accepted feature types for
> the GS lines exist (from PFAM/RFAM). The associated comment about
> this could have been prefixed with TODO - do you have a strong use
> case for custom annotations?
>

Not really, just a case where I want to add my own annotations to each
sequence in an alignment. We could support "custom" annotations directly
under the keys found in the Stockholm file, instead of trying to map them
somewhere. That would keep the PFAM/RFAM keys "mappable" but extend the
format if people want to add extra things. It's a shame such an
annotation-friendly format can only take "official" annotations..
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