[Biopython] SeqIO parser error
Michael S. Koeris
michael.koeris at gmail.com
Fri Sep 25 15:25:00 UTC 2009
Hi,
I'm just getting acquainted with Sequence Objects and records and so
forth. I tried some very basic code from the tutorial and I get an
error when I run this:
from Bio import Entrez, SeqIO
gi_list = ['224589821', '224514694', '164698032', '157812089',
'157734174']
gi_str = ",".join(gi_list)
handle = Entrez.efetch(db="nuccore", id=gi_str, rettype="gb")
records = SeqIO.parse(handle, "gb")
for record in records:
print "%s, length %i, with %i features" \
%(record.name, len(record), len(record.features))
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in
parse_records
record = self.parse(handle, do_features)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
python2.6/site-packages/Bio/GenBank/Scanner.py", line 403, in parse
if self.feed(handle, consumer, do_features) :
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
python2.6/site-packages/Bio/GenBank/Scanner.py", line 381, in feed
self._feed_misc_lines(consumer, misc_lines)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
python2.6/site-packages/Bio/GenBank/Scanner.py", line 1142, in
_feed_misc_lines
consumer.contig_location(contig_location)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
python2.6/site-packages/Bio/GenBank/__init__.py", line 987, in
contig_location
self.location(content)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
python2.6/site-packages/Bio/GenBank/__init__.py", line 689, in location
self._set_location_info(parse_info, self._cur_feature)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
python2.6/site-packages/Bio/GenBank/__init__.py", line 797, in
_set_location_info
self._set_function(parse_info, cur_feature)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
python2.6/site-packages/Bio/GenBank/__init__.py", line 720, in
_set_function
self._set_ordering_info(function, cur_feature)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/
python2.6/site-packages/Bio/GenBank/__init__.py", line 764, in
_set_ordering_info
feature_start = cur_feature.sub_features[0].location.start
AttributeError: 'PositionGap' object has no attribute 'start'
Any help is most appreciated.
Mike
--
Michael S. Koeris
michael.koeris at gmail.com
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