#!/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()