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#!/usr/bin/env python

# This code is part of the Biopython distribution and governed by its

# license. Please see the LICENSE file that should have been included

# as part of this package.

"""Check for the ability to read and write identical GenBank records.

This script takes as input a single file to be tested for reading records.

It will run through this file and check that the output of the parsed and

printed record matches the original record.

Usage:

python check_output.py <name of file to parse>

"""

# standard modules

import gzip

import os

import sys

from io import StringIO

# biopython

from Bio import GenBank

def do_comparison(good_record, test_record):

"""Compare two records to see if they are the same.

This compares the two GenBank record, and will raise an AssertionError

if two lines do not match, showing the non-matching lines.

"""

good_handle = StringIO(good_record)

test_handle = StringIO(test_record)

while True:

good_line = good_handle.readline()

test_line = test_handle.readline()

if not good_line and not test_line:

break

if not good_line:

if good_line.strip():

raise AssertionError(f"Extra info in Test: `{test_line}`")

if not test_line:

if test_line.strip():

raise AssertionError(f"Extra info in Expected: `{good_line}`")

assert test_line == good_line, (

"Expected does not match Test.\n"

f"Expect:`{good_line}`\nTest :`{test_line}`\n"

)

def write_format(file):

"""Write a GenBank record from a Genbank file and compare them."""

record_parser = GenBank.RecordParser(debug_level=2)

print("Testing GenBank writing for %s..." % os.path.basename(file))

# be able to handle gzipped files

if ".gz" in file:

cur_handle = gzip.open(file, "rb")

compare_handle = gzip.open(file, "rb")

else:

cur_handle = open(file)

compare_handle = open(file)

iterator = GenBank.Iterator(cur_handle, record_parser)

compare_iterator = GenBank.Iterator(compare_handle)

while True:

cur_record = next(iterator)

compare_record = next(compare_iterator)

if cur_record is None or compare_record is None:

break

# print("\tTesting for %s" % cur_record.version)

output_record = str(cur_record) + "\n"

try:

do_comparison(compare_record, output_record)

except AssertionError as msg:

print(f"\tTesting for {cur_record.version}")

print(msg)

cur_handle.close()

compare_handle.close()

if __name__ == "__main__":

if len(sys.argv) != 2:

print(__doc__)

sys.exit()

write_format(sys.argv[1])

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