[Biopython] GFF parsing with biopython

[Mic]

Thank you.



On Wed, May 1, 2013 at 8:04 PM, Brad Chapman <chapmanb at 50mail.com> wrote:

>
> Mic;
> (moving to galaxy-dev list so folks there can follow, but future
> questions are more appropriate for the Biopython list only since
> this isn't a Galaxy question)
>
> > I have the following GFF file from a SNAP
> >
> > X1       SNAP    Einit   2579    2712    -3.221  +       .
> X1-snap.1
> [...]
> > With the code below I have tried to parse the above GFF file
>
> The attributes you're missing are parts of the feature, not the
> SeqRecord itself, which is why you're seeing attribute error. Here's a
> full example that pulls all of the information from an example line:
>
> from BCBio import GFF
>
> in_file = "snap.gff"
> with open(in_file) as in_handle:
>     for rec in GFF.parse(in_handle):
>         feature = rec.features[0]
>         print rec.id
>         print feature.qualifiers["source"][0]
>         print feature.type
>         print feature.location.start
>         print feature.location.end
>         print feature.qualifiers["score"][0]
>         print feature.location.strand
>         print feature.qualifiers.get("X1-snap.1", [None])[0]
>
> which outputs:
>
> X1
> SNAP
> Einit
> 2578
> 2712
> -3.221
> 1
> true
>
> Hope this helps,
> Brad
>