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#
# 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
import os
import unittest
import tempfile
# Biopython Bio.KEGG.KGML (?)
from Bio.KEGG.KGML.KGML_parser import read
class PathwayData:
"""Convenience structure for testing pathway data."""
def __init__(
self,
infilename,
outfilename,
element_counts,
pathway_image,
show_pathway_image=False,
):
"""Initialize."""
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):
"""KGML checks using ko01100 metabolic map.
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
# Turn black code style off
# fmt: off
self.ko_ids = {
"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"
}
# Turn black code style on
# fmt: on
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) 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) 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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