[Biopython-dev] GTF (T not F)

[Brad Chapman]

Tiago;

> I've been noticing that there has been some work with GFF files around here.
> I've done a parser for GTF files ( http://mblab.wustl.edu/GTF22.html )
> and I was wondering if someone would find interest in it?

The GFF parser should parse the GTF variant as well:

http://github.com/chapmanb/bcbb/tree/master/gff/

If it is having trouble on any specific files please send them along
and I'll be happy to have a look.

> My knowledge of use cases of GTF/GFF is quite limited. I've done this
> to support reading Ensembl data in the context of supporting my work
> with HapMap datasets (The related project is this:
> http://popgen.eu/soft/interPop/ ) , but I really do not know the "big
> picture" of use cases.

This looks like you've specialized the extraction to this particular
type of GFF, which could be useful for folks dealing with the same
specific files you are. The GFF parser is more general and returns
Biopython SeqFeature objects, so you could use it to actually do the
parse part, and then provide your specific extraction and storage on
top of that.

Brad