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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
143 lines
3.5 KiB
Python
143 lines
3.5 KiB
Python
# Copyright 2022 by Valentin Vareskic (valentin.vareskic@gmail.com).
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# All rights reserved. This code is part of the Biopython distribution
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# and governed by its license. Please see the LICENSE file that should
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# have been included as part of this package.
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"""Tests for PDB PSEA."""
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import io
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import os
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import sys
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import unittest
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from subprocess import getoutput
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from Bio import MissingExternalDependencyError
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from Bio.PDB import PDBParser
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from Bio.PDB.PSEA import PSEA
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from Bio.PDB.PSEA import psea
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from Bio.PDB.PSEA import psea2HEC
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from Bio.PDB.PSEA import run_psea
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os.environ["LANG"] = "C"
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cmd_output = getoutput("psea -h")
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if not cmd_output.startswith("o---"):
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raise MissingExternalDependencyError(
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"Download and install psea from "
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"ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/p-sea/. "
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"Make sure that psea is on path"
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)
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def remove_sea_files():
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for file in os.listdir():
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if file.endswith(".sea"):
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os.remove(file)
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class TestPDBPSEA(unittest.TestCase):
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def tearDown(self):
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remove_sea_files()
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def test_run_psea_verbose(self):
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captured_ouput = io.StringIO()
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sys.stdout = captured_ouput
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psae_run = run_psea("PDB/1A8O.pdb", verbose=True)
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sys.stdout = sys.__stdout__
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self.assertEqual(psae_run, "1A8O.sea")
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self.assertTrue(captured_ouput.getvalue())
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def test_run_psea_quiet(self):
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captured_ouput = io.StringIO()
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sys.stdout = captured_ouput
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psae_run = run_psea("PDB/1A8O.pdb", verbose=False)
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sys.stdout = sys.__stdout__
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self.assertEqual(psae_run, "1A8O.sea")
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self.assertFalse(captured_ouput.getvalue())
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def test_psea(self):
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psae_run = psea("PDB/2BEG.pdb")
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self.assertEqual(psae_run, "ccccbbbbbbbccccbbbbbbbbbbc")
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def test_psea_2HEC(self):
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seq = psea("PDB/2BEG.pdb")
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psae_run = psea2HEC(seq)
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self.assertEqual(
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psae_run,
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[
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"C",
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"C",
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"C",
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"C",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"C",
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"C",
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"C",
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"C",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"C",
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],
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)
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class TestPSEA(unittest.TestCase):
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def tearDown(self):
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remove_sea_files()
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def test_get_seq(self):
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p = PDBParser()
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s = p.get_structure("X", "PDB/2BEG.pdb")
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psea_class = PSEA(s[0], "PDB/2BEG.pdb")
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self.assertEqual(
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psea_class.get_seq(),
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[
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"C",
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"C",
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"C",
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"C",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"C",
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"C",
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"C",
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"C",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"E",
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"C",
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],
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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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