[Biopython] Error while parsing bgk file
ning luwen
bioinformaticsing at gmail.com
Thu Jul 19 03:36:19 UTC 2012
Hi everyone,
A error encountered when i parse a gbk file.
the error message as follow:
Traceback (most recent call last):
File "stat_refseq_gbs.py", line 10, in <module>
for seq in f:
File "/media/disk2/bio/bin/lib/python2.7/site-packages/Bio/SeqIO/__init__.py",
line 537, in parse
for r in i:
File "/media/disk2/bio/bin/lib/python2.7/site-packages/Bio/GenBank/Scanner.py",
line 445, in parse_records
record = self.parse(handle, do_features)
File "/media/disk2/bio/bin/lib/python2.7/site-packages/Bio/GenBank/Scanner.py",
line 428, in parse
if self.feed(handle, consumer, do_features):
File "/media/disk2/bio/bin/lib/python2.7/site-packages/Bio/GenBank/Scanner.py",
line 400, in feed
self._feed_feature_table(consumer, self.parse_features(skip=False))
File "/media/disk2/bio/bin/lib/python2.7/site-packages/Bio/GenBank/Scanner.py",
line 350, in _feed_feature_table
consumer.location(location_string)
File "/media/disk2/bio/bin/lib/python2.7/site-packages/Bio/GenBank/__init__.py",
line 970, in location
int(e),
ValueError: invalid literal for int() with base 10: '68452073^68452074'
the file parsed is ref_GRCh37.p5, the biopython version is 1.60, the
lines cause the error may be:
V_segment complement(68451760..68452073^68452074)
CDS complement(<68451760..68452072^68452073)
--
regards,
luwen ning
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