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// Problem with GFF parser by BCBio
// April 21, 2011 at 5:50 AM

http://stackoverflow.com/questions/5742379/problem-with-gff-parser-by-bcbio
Hi,

I am trying to parse a GFF file using the BCBio GFF parser and I get the following error. Can anybody help me in resolving this problem?

Traceback (most recent call last):
  File "gff_parse.py", line 6, in 
    for rec in GFF.parse(in_handle):
  File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 709, in parse
  File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 299, in parse_in_parts
  File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 320, in parse_simple
  File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 603, in _gff_process
  File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 634, in _lines_to_out_info
  File "build/bdist.linux-x86_64/egg/BCBio/GFF/GFFParser.py", line 183, in _gff_line_map
ValueError: invalid literal for int() with base 10: 'New Start'

Here is my code:

from BCBio import GFF

in_file = "infile.gff"

in_handle = open(in_file)

for rec in GFF.parse(in_handle):

 print rec


in_handle.close()

Thanks 
Tulika


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