BCBio的GFF解析器问题

Question

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 <module>
    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

Answer 1

How did you generate the GFF file? It appears to contain at least one invalid line. The fourth column should contain integers for the start coordinate of a feature; the error message indicates it contains the value 'New Start' instead.

The GFF3 specification page has some examples of valid GFF, and the online validator can help with debugging formatting issues like this.