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 fileThe 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