[Biopython-dev] [Biopython - Bug #3197] SeqIO parse error with some genbank files

[redmine at redmine.open-bio.org]

Issue #3197 has been updated by Cedar McKay.


Peter, thanks as always for your quick and helpful response! I've emailed NCBI about these apparently illegal files, and I'll update this bug when I get a reply. In the meantime, I'm going to go ahead and use your hacked up version. Thanks!
----------------------------------------
Bug #3197: SeqIO parse error with some genbank files
https://redmine.open-bio.org/issues/3197

Author: Cedar McKay
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 1.56
URL: 


I've found a file that seems to choke SeqIO genbank parsing.  I downloaded this file straight from NCBI, so it should be a good file. I've found a couple of other files that do the same thing. I reproduced this bug on another machine, also with biopython 1.56. I am able to successfully parse other genbank files. Maybe it has something to do with that very long location?  Please let me know if I can provide any other information!
Thanks!

Cedar


>>> from Bio import SeqIO
>>> record = SeqIO.read('./Acorus_americanus_NC_010093.gb', 'genbank')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 597, in read
    first = iterator.next()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/SeqIO/__init__.py", line 525, in parse
    for r in i:
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 437, in parse_records
    record = self.parse(handle, do_features)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 420, in parse
    if self.feed(handle, consumer, do_features):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 392, in feed
    self._feed_feature_table(consumer, self.parse_features(skip=False))
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/Scanner.py", line 344, in _feed_feature_table
    consumer.location(location_string)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Bio/GenBank/__init__.py", line 975, in location
    raise LocationParserError(location_line)
Bio.GenBank.LocationParserError: order(join(42724..42726,43455..43457),43464..43469,43476..43481,43557..43562,43569..43574,43578..43583,43677..43682,44434..44439)



-- 
You have received this notification because you have either subscribed to it, or are involved in it.
To change your notification preferences, please click here and login: http://redmine.open-bio.org