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#!/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
from __future__ import print_function
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 True:
have_record = 0
while have_record == 0:
try:
cur_record = next(iterator)
have_record = 1
except GenBank.ParserFailureError as msg:
print("Parsing Problem: %s" % msg)
sys.exit()
if cur_record is None:
break
print("Successfully parsed record %s" % cur_record.id)
if verbose:
print("***Record")
print("Seq: %s" % cur_record.seq)
print("Id: %s" % cur_record.id)
print("Name: %s" % cur_record.name)
print("Description: %s" % cur_record.description)
print("Annotations: %s" % cur_record.annotations)
print("Feaures")
for feature in cur_record.features:
print(feature)
handle.close()
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