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

[redmine at redmine.open-bio.org]

Issue #3197 has been updated by Peter Cock.


Two more examples from the NCBI Bacteria FTP site, reported by Tim te Beek on our mailing list:

http://lists.open-bio.org/pipermail/biopython-dev/2011-July/009018.html
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Desulfurococcus_kamchatkensis_1221n_uid59133/NC_011766.gbk

LOCUS       NC_011766            1365223 bp    DNA     circular BCT 20-MAY-2011
DEFINITION  Desulfurococcus kamchatkensis 1221n chromosome, complete genome.
ACCESSION   NC_011766
VERSION     NC_011766.1  GI:218883314
DBLINK      Project: 59133
KEYWORDS    .
SOURCE      Desulfurococcus kamchatkensis 1221n
...
     misc_feature    complement(order(1078481..1078483,join(1078778,
                     1078800..1078810)))
                     /locus_tag="DKAM_1147"
                     /note="active site"
                     /db_xref="CDD:73252"

http://lists.open-bio.org/pipermail/biopython-dev/2011-July/009019.html
ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Saccharopolyspora_erythraea_NRRL_2338_uid62947/NC_009142.gbk

LOCUS       NC_009142            8212805 bp    DNA     circular BCT 14-FEB-2011
DEFINITION  Saccharopolyspora erythraea NRRL 2338 chromosome, complete genome.
ACCESSION   NC_009142
VERSION     NC_009142.1  GI:134096620
DBLINK      Project: 62947
KEYWORDS    complete genome.
SOURCE      Saccharopolyspora erythraea NRRL 2338
...
     misc_feature    order(2409324..2409326,2409399..2409401,2409528..2409533,
                     2409619..2409624,2409679..2409681,2409748..2409753,
                     2409754..2409759,2409835..2409837,join(2409886..2409890,
                     2409892..2409898),2409911..2409913,2409920..2409925)
                     /locus_tag="SACE_2218"
                     /note="active site"
                     /db_xref="CDD:119408"
     misc_feature    order(2409324..2409326,2409399..2409401,2409528..2409530)
                     /locus_tag="SACE_2218"
                     /note="catalytic tetrad; other site"
                     /db_xref="CDD:119408"


----------------------------------------
Bug #3197: SeqIO parse error with some genbank files
https://redmine.open-bio.org/issues/3197

Author: Cedar McKay
Status: Resolved
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)



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