[Biopython-dev] [Bug 2825] New: SeqIO does not successfully parse Genbank records related to whole genome sequencing deposits, as Did not recognise the LOCUS line layout

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2825

           Summary: SeqIO does not successfully parse Genbank records
                    related to whole genome sequencing deposits, as Did not
                    recognise the LOCUS line layout
           Product: Biopython
           Version: 1.49
          Platform: All
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: david.wyllie at ndm.ox.ac.uk


Hi

I'm using the BioPython distribution 1.49 obtained as a Package using the
Ubuntu 9 synaptic package manager.  The below describes the problem:

NCBI has a record type which describes the contents of whole-genome sequencing
projects.  The record doesn't itself contain sequence, by constrast to most
genbank records.

this URL gives an example
http://www.ncbi.nlm.nih.gov/nuccore/162285818
should the SeqIO parser be able to read this? it cannot.  Here is an example:

# import modules
from Bio import Entrez
from Bio import SeqIO

# read the record from NCBI, print out the contents.
handle = Entrez.efetch(db="nucleotide", rettype="gb", id="162285818")
masterrecord=handle.readlines()
for line in masterrecord:
        print line
handle.close()

# let's read it again, and try to parse with with SeqIO.
handle = Entrez.efetch(db="nucleotide", rettype="gb", id="162285818")

# this line causes the crash
seq_record = SeqIO.read(handle, "genbank")

handle.close()

# fails.  the traceback reads
"""
Traceback (most recent call last):
  File "bugreport.py", line 25, in <module>
    seq_record = SeqIO.read(handle, "genbank")
  File "/var/lib/python-support/python2.6/Bio/SeqIO/__init__.py", line 435, in
read
    first = iterator.next()
  File "/var/lib/python-support/python2.6/Bio/GenBank/Scanner.py", line 410, in
parse_records
    record = self.parse(handle)
  File "/var/lib/python-support/python2.6/Bio/GenBank/Scanner.py", line 393, in
parse
    if self.feed(handle, consumer) :
  File "/var/lib/python-support/python2.6/Bio/GenBank/Scanner.py", line 360, in
feed
    self._feed_first_line(consumer, self.line)
  File "/var/lib/python-support/python2.6/Bio/GenBank/Scanner.py", line 907, in
_feed_first_line
    raise ValueError('Did not recognise the LOCUS line layout:\n' + line)
ValueError: Did not recognise the LOCUS line layout:
LOCUS       ABIN01000000             353 rc    DNA     linear   BCT 10-DEC-2007
"""

# by contrast, reading one of the constituent genbank records, like this one
# http://www.ncbi.nlm.nih.gov/nuccore/162285817
# works correctly;

handle = Entrez.efetch(db="nucleotide", rettype="gb", id="162285817")
seq_record = SeqIO.read(handle, "genbank")
handle.close()
print "Successfully loaded record GI=162285817"
print seq_record.description


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