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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
141 lines
4.8 KiB
Python
141 lines
4.8 KiB
Python
# Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com)
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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 PAML tools module."""
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import os
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import sys
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import unittest
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from Bio import MissingExternalDependencyError
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from Bio.Phylo.PAML import baseml
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from Bio.Phylo.PAML import codeml
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from Bio.Phylo.PAML import yn00
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def is_exe(filepath):
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"""Test if a file is an executable."""
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return os.path.exists(filepath) and os.access(filepath, os.X_OK)
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def which(program):
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"""Find the path to an executable."""
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filepath, filename = os.path.split(program)
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os_path = os.environ["PATH"].split(os.pathsep)
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if sys.platform == "win32":
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try:
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# This can vary depending on the Windows language.
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prog_files = os.environ["PROGRAMFILES"]
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except KeyError:
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prog_files = r"C:\Program Files"
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# For Windows, the user is instructed to move the programs to a folder
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# and then to add the folder to the system path. Just in case they didn't
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# do that, we can check for it in Program Files.
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likely_dirs = [
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"", # Current dir
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prog_files,
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os.path.join(prog_files, "paml41"),
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os.path.join(prog_files, "paml43"),
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os.path.join(prog_files, "paml44"),
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os.path.join(prog_files, "paml45"),
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] + sys.path
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os_path.extend(likely_dirs)
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for path in os.environ["PATH"].split(os.pathsep):
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exe_file = os.path.join(path, program)
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if is_exe(exe_file):
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return exe_file
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return None
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# Find the PAML binaries
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if sys.platform == "win32":
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binaries = ["codeml.exe", "baseml.exe", "yn00.exe"]
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else:
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binaries = ["codeml", "baseml", "yn00"]
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for binary in binaries:
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if which(binary) is None:
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raise MissingExternalDependencyError(
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"Install PAML if you want to use the Bio.Phylo.PAML wrapper."
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)
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class Common(unittest.TestCase):
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"""Base class for PAML unit tests."""
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del_files = []
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def __del__(self):
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"""Just in case tool creates some junk files, do a clean-up."""
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del_files = self.del_files
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for filename in del_files:
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if os.path.exists(filename):
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os.remove(filename)
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class CodemlTest(Common):
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"""Tests for PAML tool codeml."""
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def setUp(self):
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self.cml = codeml.Codeml()
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def testCodemlBinary(self):
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"""Check codeml runs, generates correct output, and is the correct version."""
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ctl_file = os.path.join("PAML", "Control_files", "codeml", "codeml.ctl")
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self.cml.read_ctl_file(ctl_file)
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self.cml.alignment = os.path.join("PAML", "Alignments", "alignment.phylip")
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self.cml.tree = os.path.join("PAML", "Trees", "species.tree")
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self.cml.out_file = os.path.join("PAML", "temp.out")
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self.cml.working_dir = os.path.join("PAML", "codeml_test")
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results = self.cml.run()
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self.assertGreater(results["version"], "4.0")
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self.assertIn("NSsites", results)
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self.assertEqual(len(results["NSsites"]), 1)
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self.assertEqual(len(results["NSsites"][0]), 5)
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class BasemlTest(Common):
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"""Tests for PAML tool baseml."""
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def setUp(self):
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self.bml = baseml.Baseml()
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def testBasemlBinary(self):
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"""Check baseml runs, generates correct output, and is the correct version."""
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ctl_file = os.path.join("PAML", "Control_files", "baseml", "baseml.ctl")
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self.bml.read_ctl_file(ctl_file)
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self.bml.alignment = os.path.join("PAML", "Alignments", "alignment.phylip")
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self.bml.tree = os.path.join("PAML", "Trees", "species.tree")
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self.bml.out_file = os.path.join("PAML", "temp.out")
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self.bml.working_dir = os.path.join("PAML", "baseml_test")
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results = self.bml.run()
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self.assertGreater(results["version"], "4.0")
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self.assertIn("parameters", results)
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self.assertEqual(len(results["parameters"]), 5)
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class Yn00Test(Common):
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"""Tests for PAML tool yn00."""
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def setUp(self):
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self.yn = yn00.Yn00()
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def testYn00Binary(self):
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"""Check yn00 binary runs and generates correct output.
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yn00 output does not specify the version number.
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"""
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ctl_file = os.path.join("PAML", "Control_files", "yn00", "yn00.ctl")
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self.yn.read_ctl_file(ctl_file)
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self.yn.alignment = os.path.join("PAML", "Alignments", "alignment.phylip")
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self.yn.out_file = os.path.join("PAML", "temp.out")
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self.yn.working_dir = os.path.join("PAML", "yn00_test")
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results = self.yn.run()
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self.assertEqual(len(results), 5)
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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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