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#!/usr/bin/env python
#
# Copyright 2013 by Leighton Pritchard. All rights reserved.
# 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.
""" Tests for general functionality of the KGML parser and pathway model
"""
# Builtins
from __future__ import with_statement
import os
import unittest
import tempfile
# Biopython Bio.KEGG.KGML (?)
from Bio.KEGG.KGML.KGML_parser import read
class PathwayData(object):
""" Convenience structure for testing pathway data
"""
def __init__(self, infilename, outfilename, element_counts,
pathway_image, show_pathway_image=False):
self.infilename = infilename
self.outfilename = outfilename
self.element_counts = element_counts
self.pathway_image = pathway_image
self.show_pathway_image = show_pathway_image
class KGMLPathwayTest(unittest.TestCase):
""" Import the ko01100 metabolic map from a local .xml KGML file, and from
the KEGG site, and write valid KGML output for each
"""
def setUp(self):
# Does our output director exist? If not, create it
if not os.path.isdir('KEGG'):
os.mkdir('KEGG')
# Define some data to work with as a list of tuples:
# (infilename, outfilename, (entry_count, ortholog_count,
# compound_count, map_counts), pathway_image,
# show_image_map)
self.data = [PathwayData(os.path.join("KEGG", "ko01100.xml"),
tempfile.gettempprefix() + ".ko01100.kgml",
(3628, 1726, 1746, 149),
os.path.join("KEGG", "map01100.png")),
PathwayData(os.path.join("KEGG", "ko03070.xml"),
tempfile.gettempprefix() + ".ko03070.kgml",
(81, 72, 8, 1),
os.path.join("KEGG", "map03070.png"),
True)]
# A list of KO IDs that we're going to use to modify pathway
# appearance. These are KO IDs for reactions that take part in ko00020,
# the TCA cycle
self.ko_ids = \
set(['ko:K00239', 'ko:K00240', 'ko:K00241', 'ko:K00242', 'ko:K00244',
'ko:K00245', 'ko:K00246', 'ko:K00247', 'ko:K00174', 'ko:K00175',
'ko:K00177', 'ko:K00176', 'ko:K00382', 'ko:K00164', 'ko:K00164',
'ko:K00658', 'ko:K01902', 'ko:K01903', 'ko:K01899', 'ko:K01900',
'ko:K01899', 'ko:K01900', 'ko:K00031', 'ko:K00030', 'ko:K00031',
'ko:K01648', 'ko:K00234', 'ko:K00235', 'ko:K00236', 'ko:K00237',
'ko:K01676', 'ko:K01677', 'ko:K01678', 'ko:K01679', 'ko:K01681',
'ko:K01682', 'ko:K01681', 'ko:K01682', 'ko:K01647', 'ko:K00025',
'ko:K00026', 'ko:K00024', 'ko:K01958', 'ko:K01959', 'ko:K01960',
'ko:K00163', 'ko:K00161', 'ko:K00162', 'ko:K00163', 'ko:K00161',
'ko:K00162', 'ko:K00382', 'ko:K00627', 'ko:K00169', 'ko:K00170',
'ko:K00172', 'ko:K00171', 'ko:K01643', 'ko:K01644', 'ko:K01646',
'ko:K01610', 'ko:K01596'])
def tearDown(self):
for p in self.data:
if os.path.isfile(p.outfilename):
os.remove(p.outfilename)
def test_read_and_write_KGML_files(self):
""" Read KGML from, and write KGML to, local files.
Check we read/write the correct number of elements.
"""
for p in self.data:
# Test opening file
with open(p.infilename, 'rU') as f:
pathway = read(f)
# Do we have the correct number of elements of each type
self.assertEqual((len(pathway.entries),
len(pathway.orthologs),
len(pathway.compounds),
len(pathway.maps)),
p.element_counts)
# Test writing file
with open(p.outfilename, 'w') as f:
f.write(pathway.get_KGML())
# Can we read the file we wrote?
with open(p.outfilename, 'rU') as f:
pathway = read(f)
# Do we have the correct number of elements of each type
self.assertEqual((len(pathway.entries),
len(pathway.orthologs),
len(pathway.compounds),
len(pathway.maps)),
p.element_counts)
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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