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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
132 lines
4.7 KiB
Python
132 lines
4.7 KiB
Python
# Copyright 2013 by Leighton Pritchard. All rights reserved.
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# This code is part of the Biopython distribution and governed by its
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# license. Please see the LICENSE file that should have been included
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# as part of this package.
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"""Tests for general functionality of the KGML parser and pathway model."""
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# Builtins
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import os
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import tempfile
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import unittest
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# Biopython Bio.KEGG.KGML (?)
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from Bio.KEGG.KGML.KGML_parser import read
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class PathwayData:
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"""Convenience structure for testing pathway data."""
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def __init__(
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self,
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infilename,
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outfilename,
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element_counts,
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pathway_image,
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show_pathway_image=False,
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):
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"""Initialize the class."""
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self.infilename = infilename
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self.outfilename = outfilename
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self.element_counts = element_counts
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self.pathway_image = pathway_image
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self.show_pathway_image = show_pathway_image
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class KGMLPathwayTest(unittest.TestCase):
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"""KGML checks using ko01100 metabolic map.
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Import the ko01100 metabolic map from a local .xml KGML file, and from
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the KEGG site, and write valid KGML output for each
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"""
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def setUp(self):
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# Does our output director exist? If not, create it
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if not os.path.isdir("KEGG"):
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os.mkdir("KEGG")
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# Define some data to work with as a list of tuples:
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# (infilename, outfilename, (entry_count, ortholog_count,
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# compound_count, map_counts), pathway_image,
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# show_image_map)
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self.data = [
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PathwayData(
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os.path.join("KEGG", "ko01100.xml"),
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tempfile.gettempprefix() + ".ko01100.kgml",
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(3628, 1726, 1746, 149),
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os.path.join("KEGG", "map01100.png"),
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),
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PathwayData(
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os.path.join("KEGG", "ko03070.xml"),
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tempfile.gettempprefix() + ".ko03070.kgml",
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(81, 72, 8, 1),
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os.path.join("KEGG", "map03070.png"),
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True,
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),
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]
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# A set of KO IDs that we're going to use to modify pathway
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# appearance. These are KO IDs for reactions that take part in ko00020,
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# the TCA cycle
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# Turn black code style off
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# fmt: off
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self.ko_ids = {
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"ko:K00024", "ko:K00025", "ko:K00026", "ko:K00030", "ko:K00031",
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"ko:K00161", "ko:K00162", "ko:K00163", "ko:K00164", "ko:K00169",
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"ko:K00170", "ko:K00171", "ko:K00172", "ko:K00174", "ko:K00175",
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"ko:K00176", "ko:K00177", "ko:K00234", "ko:K00235", "ko:K00236",
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"ko:K00237", "ko:K00239", "ko:K00240", "ko:K00241", "ko:K00242",
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"ko:K00244", "ko:K00245", "ko:K00246", "ko:K00247", "ko:K00382",
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"ko:K00627", "ko:K00658", "ko:K01596", "ko:K01610", "ko:K01643",
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"ko:K01644", "ko:K01646", "ko:K01647", "ko:K01648", "ko:K01676",
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"ko:K01677", "ko:K01678", "ko:K01679", "ko:K01681", "ko:K01682",
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"ko:K01899", "ko:K01900", "ko:K01902", "ko:K01903", "ko:K01958",
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"ko:K01959", "ko:K01960"
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}
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# Turn black code style on
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# fmt: on
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def tearDown(self):
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for p in self.data:
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if os.path.isfile(p.outfilename):
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os.remove(p.outfilename)
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def test_read_and_write_KGML_files(self):
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"""Read KGML from, and write KGML to, local files.
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Check we read/write the correct number of elements.
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"""
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for p in self.data:
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# Test opening file
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with open(p.infilename) as f:
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pathway = read(f)
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# Do we have the correct number of elements of each type
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self.assertEqual(
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(
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len(pathway.entries),
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len(pathway.orthologs),
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len(pathway.compounds),
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len(pathway.maps),
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),
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p.element_counts,
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)
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# Test writing file
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with open(p.outfilename, "w") as f:
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f.write(pathway.get_KGML())
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# Can we read the file we wrote?
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with open(p.outfilename) as f:
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pathway = read(f)
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# Do we have the correct number of elements of each type
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self.assertEqual(
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(
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len(pathway.entries),
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len(pathway.orthologs),
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len(pathway.compounds),
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len(pathway.maps),
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),
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p.element_counts,
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)
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if __name__ == "__main__":
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runner = unittest.TextTestRunner(verbosity=2)
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unittest.main(testRunner=runner)
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