[Biopython-dev] [Bug 2229] New: GenBank Scanner fails to scan over headers

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Mar 12 15:36:33 UTC 2007


           Summary: GenBank Scanner fails to scan over headers
           Product: Biopython
           Version: Not Applicable
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mcolosimo at mitre.org

The new GenBank code fails to read in NCBI-GenBank flat file releases, such as
gbvrl1.seq (release 158.0)

from Bio import GenBank
import sys

fh = open(sys.argv[1], 'r')
gb_iter = GenBank.Iterator(fh, GenBank.FeatureParser())
for rec in gb_iter:
    print rec.id

This fails because the first item is not 'LOCUS'. The following works.

Index: Scanner.py
RCS file: /home/repository/biopython/biopython/Bio/GenBank/Scanner.py,v
retrieving revision 1.7
diff -r1.7 Scanner.py
<                 break
>                 self.line = line
>                 return line
<                 raise SyntaxError("Expected line starting '%s', found '%s'" \
<                                   % (self.RECORD_START, line.rstrip()))
<         self.line = line
<         return line
>                 if self.debug > 1: print "Skipping line"
>         return None

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