[Biopython] Error while parsing bgk file

ning luwen bioinformaticsing at gmail.com
Wed Jul 18 23:36:19 EDT 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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