Thank you. On Wed, May 1, 2013 at 8:04 PM, Brad Chapman <chapmanb@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