[Biopython] GFF parsing with biopython
Mic
mictadlo at gmail.com
Fri May 3 05:08:18 UTC 2013
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
>
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