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Sourcecode: python-biopython version File versions

find_parser_problems.py

#!/usr/bin/env python
"""Find GenBank records that the parser has problems with within a big file.

This is meant to make it easy to get accession numbers for records that
don't parse properly.

Usage:
find_parser_problems.py <GenBank file to parse>
"""
# standard library
import sys

# GenBank
from Bio import GenBank

verbose = 0

if len(sys.argv) != 2:
    print "Usage ./find_parser_problems <GenBank file to parse>"
    sys.exit()

feature_parser = GenBank.FeatureParser(debug_level = 0)
parser = GenBank.ErrorParser(feature_parser)

handle = open(sys.argv[1], 'r')
iterator = GenBank.Iterator(handle, parser, has_header = 1)

while 1:
    have_record = 0
    
    while have_record == 0:
        try:
            cur_record = iterator.next()
            have_record = 1
        except GenBank.ParserFailureError, msg:
            print "Parsing Problem:", msg
            sys.exit()

    if cur_record is None:
        break

    print "Successfully parsed record", cur_record.id
    
    if verbose:
        print "***Record"
        print "Seq:", cur_record.seq
        print "Id:", cur_record.id
        print "Name:", cur_record.name
        print "Description", cur_record.description
        print "Annotations", cur_record.annotations
        print "Feaures"
        for feature in cur_record.features:
            print feature
                
handle.close()
    



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