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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
185 lines
7.0 KiB
Python
185 lines
7.0 KiB
Python
# Copyright 2009 by Cymon J. Cox. 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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"""Unittests for Bio.Align.Applications interface for TCOFFEE."""
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import os
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import sys
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import unittest
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import warnings
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from Bio import AlignIO
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from Bio import BiopythonDeprecationWarning
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from Bio import MissingExternalDependencyError
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from Bio import SeqIO
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with warnings.catch_warnings():
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warnings.simplefilter("ignore", category=BiopythonDeprecationWarning)
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from Bio.Align.Applications import TCoffeeCommandline
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# Try to avoid problems when the OS is in another language
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os.environ["LANG"] = "C"
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t_coffee_exe = None
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if sys.platform == "win32":
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raise MissingExternalDependencyError("Testing TCOFFEE on Windows not supported yet")
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else:
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from subprocess import getoutput
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output = getoutput("t_coffee -version")
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if "not found" not in output and "not recognized" not in output:
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if "t_coffee" in output.lower() or "t-coffee" in output.lower():
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t_coffee_exe = "t_coffee"
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if not t_coffee_exe:
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raise MissingExternalDependencyError(
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"Install TCOFFEE if you want to use the Bio.Align.Applications wrapper."
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)
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class TCoffeeApplication(unittest.TestCase):
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def setUp(self):
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self.infile1 = "Fasta/fa01"
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# TODO: Use a temp dir for the output files:
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self.outfile1 = "fa01.aln"
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self.outfile2 = "fa01.html" # Written by default when no output set
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self.outfile3 = "Fasta/tc_out.pir"
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self.outfile4 = "Fasta/tc_out.aln"
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self.outfile5 = "Fasta/tc_out.phy"
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self.outfile6 = "Fasta/tc_out.msf"
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def tearDown(self):
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if os.path.isfile(self.outfile1):
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os.remove(self.outfile1)
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if os.path.isfile(self.outfile2):
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os.remove(self.outfile2)
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if os.path.isfile(self.outfile3):
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os.remove(self.outfile3)
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if os.path.isfile(self.outfile4):
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os.remove(self.outfile4)
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if os.path.isfile(self.outfile5):
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os.remove(self.outfile5)
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def test_TCoffee_fasta(self):
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"""Round-trip through app and read clustal alignment from file."""
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cmdline = TCoffeeCommandline(t_coffee_exe, infile=self.infile1)
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self.assertEqual(str(cmdline), t_coffee_exe + " -infile Fasta/fa01")
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stdout, stderr = cmdline()
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self.assertTrue(stderr.strip().startswith("PROGRAM: T-COFFEE"))
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align = AlignIO.read(self.outfile1, "clustal")
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records = list(SeqIO.parse(self.infile1, "fasta"))
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self.assertEqual(len(records), len(align))
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for old, new in zip(records, align):
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self.assertEqual(old.id, new.id)
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self.assertEqual(
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str(new.seq).replace("-", ""), str(old.seq).replace("-", "")
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)
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def test_TCoffee_pir(self):
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"""Round-trip through app and read pir alignment from file."""
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cmdline = TCoffeeCommandline(t_coffee_exe, quiet=True)
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cmdline.infile = self.infile1
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cmdline.outfile = self.outfile3
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cmdline.output = "pir_aln"
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self.assertEqual(
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str(cmdline),
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t_coffee_exe
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+ " -output pir_aln -infile Fasta/fa01 -outfile Fasta/tc_out.pir -quiet",
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)
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stdout, stderr = cmdline()
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# Can get warnings in stderr output
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self.assertNotIn("error", stderr.lower(), stderr)
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align = AlignIO.read(self.outfile3, "pir")
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records = list(SeqIO.parse(self.infile1, "fasta"))
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self.assertEqual(len(records), len(align))
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for old, new in zip(records, align):
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self.assertEqual(old.id, new.id)
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self.assertEqual(
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str(new.seq).replace("-", ""), str(old.seq).replace("-", "")
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)
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def test_TCoffee_clustalw(self):
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"""Round-trip through app and read clustalw alignment from file."""
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cmdline = TCoffeeCommandline(t_coffee_exe, gapopen=-2)
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cmdline.infile = self.infile1
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cmdline.outfile = self.outfile4
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cmdline.set_parameter("output", "clustalw_aln")
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cmdline.outorder = "input"
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cmdline.set_parameter("gapext", -5)
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cmdline.type = "protein"
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self.assertEqual(
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str(cmdline),
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t_coffee_exe
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+ " -output clustalw_aln -infile Fasta/fa01 -outfile Fasta/tc_out.aln "
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"-type protein -outorder input -gapopen -2 -gapext -5",
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)
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stdout, stderr = cmdline()
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self.assertTrue(stderr.strip().startswith("PROGRAM: T-COFFEE"))
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align = AlignIO.read(self.outfile4, "clustal")
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records = list(SeqIO.parse(self.infile1, "fasta"))
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self.assertEqual(len(records), len(align))
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for old, new in zip(records, align):
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self.assertEqual(old.id, new.id)
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self.assertEqual(
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str(new.seq).replace("-", ""), str(old.seq).replace("-", "")
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)
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def test_TCoffee_phylip(self):
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"""Round-trip through app and read PHYLIP alignment from file."""
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cmdline = TCoffeeCommandline(
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t_coffee_exe,
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infile=self.infile1,
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outfile=self.outfile5,
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quiet=True,
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output="phylip_aln",
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)
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self.assertEqual(
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str(cmdline),
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t_coffee_exe + " -output phylip_aln "
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"-infile Fasta/fa01 -outfile Fasta/tc_out.phy -quiet",
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)
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stdout, stderr = cmdline()
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# Can get warnings in stderr output
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self.assertNotIn("error", stderr.lower(), stderr)
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align = AlignIO.read(self.outfile5, "phylip")
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records = list(SeqIO.parse(self.infile1, "fasta"))
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self.assertEqual(len(records), len(align))
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for old, new in zip(records, align):
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# TCoffee does strict 10 character truncation as per original PHYLIP
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self.assertEqual(old.id[:10], new.id[:10])
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self.assertEqual(
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str(new.seq).replace("-", ""), str(old.seq).replace("-", "")
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)
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def test_TCoffee_msf(self):
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"""Round-trip through app and read GCG MSF alignment from file."""
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cmdline = TCoffeeCommandline(
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t_coffee_exe,
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infile=self.infile1,
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outfile=self.outfile6,
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quiet=True,
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output="msf_aln",
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)
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self.assertEqual(
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str(cmdline),
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t_coffee_exe
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+ " -output msf_aln -infile Fasta/fa01 -outfile Fasta/tc_out.msf -quiet",
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)
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stdout, stderr = cmdline()
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# Can get warnings in stderr output
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self.assertNotIn("error", stderr.lower(), stderr)
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align = AlignIO.read(self.outfile6, "msf")
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records = list(SeqIO.parse(self.infile1, "fasta"))
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self.assertEqual(len(records), len(align))
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for old, new in zip(records, align):
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self.assertEqual(old.id, new.id)
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self.assertEqual(
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str(new.seq).replace("-", ""), str(old.seq).replace("-", "")
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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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