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#!/usr/bin/env python
#-----------------------------------------------------------------------------
# Copyright (c) 2013, The PyNAST Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
#-----------------------------------------------------------------------------
from __future__ import division
from tempfile import NamedTemporaryFile
from os import remove
from cogent import LoadSeqs, DNA
from cogent.util.unit_test import TestCase, main
from cogent.parse.fasta import MinimalFastaParser
from pynast.logger import NastLogger
from pynast.util import get_pynast_temp_dir
class NastLoggerTests(TestCase):
"""Tests of the PyNAST logging class"""
def setUp(self):
# Note that delete = False here because we don't want these to
# be deleted when they are closed (since we need to pass
# the filepaths around after we write and close them). The files
# are deleted explicitly at the end of the test.
self.file = NamedTemporaryFile(prefix='NastLoggerTest',
suffix='.log',
dir=get_pynast_temp_dir(),
delete=False)
self.file.close()
self.filename = self.file.name
def tearDown(self):
try:
remove(self.filename)
except OSError:
pass
def test_init(self):
"""NastLogger.__init__ should store log filename in Filename attribute"""
null_logger = NastLogger()
self.assertEqual(null_logger.Filename, None)
file_logger = NastLogger(self.filename)
self.assertEqual(file_logger.Filename, self.filename)
def test_header(self):
"""NastLogger.__init__ should write correct header to log file"""
logger = NastLogger(self.filename)
f = open(self.filename, 'r')
header = f.readline()
f.close()
exp_header = (
'candidate sequence ID\tcandidate nucleotide count\terrors\t'
'template ID\tBLAST percent identity to template\t'
'candidate nucleotide count post-NAST\n'
)
self.assertEqual(header, exp_header)
def test_record(self):
"""NastLogger.__init__ should record tab-separated values to log file"""
logger = NastLogger(self.filename)
logger.record('hello', 'world')
f = open(self.filename, 'r')
obs_header = f.readline()
obs_message = f.readline()
f.close()
self.assertEqual(obs_message, 'hello\tworld\n')
if __name__ == "__main__":
main()
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