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Sourcecode: python-biopython version File versions  Download package


#!/usr/bin/env python
"""Display the SeqFeatures produced by the parser.

This produces a ton of output so it is possible to hand check what is
produced by the parser with the original GenBank file to make sure
everything is being parsed and output properly.

./check_output.py <GenBank file to parse>

# standard library
import sys

# GenBank stuff to test
from Bio import GenBank

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

parser = GenBank.FeatureParser(debug_level = 2)

handle = open(sys.argv[1], 'r')

iterator = GenBank.Iterator(handle, parser)

while 1:
    cur_record = iterator.next()

    if not(cur_record):
    print "***Record"
    print "Seq:", cur_record.seq
    print "Id:", cur_record.id
    print "Name:", cur_record.name
    print "Description", cur_record.description
    print "Annotations****"
    for annotation_key in cur_record.annotations.keys():
        if annotation_key != 'references':
            print "Key: %s" % annotation_key
            print "Value: %s" % cur_record.annotations[annotation_key]
            print "References*"
            for reference in cur_record.annotations[annotation_key]:
                print str(reference)
    print "Feaures"
    for feature in cur_record.features:
        print feature


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