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# Copyright 2009 by Cymon J. Cox. 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.
"""Unittests for Bio.Align.Applications interface for PROBCONS."""
import sys
import os
import unittest
from io import StringIO
from Bio import AlignIO, SeqIO, MissingExternalDependencyError
from Bio.Align.Applications import ProbconsCommandline
# Try to avoid problems when the OS is in another language
os.environ["LANG"] = "C"
probcons_exe = None
if sys.platform == "win32":
raise MissingExternalDependencyError("PROBCONS not available on Windows")
else:
from subprocess import getoutput
output = getoutput("probcons")
if "not found" not in output and "not recognized" not in output:
if "probcons" in output.lower():
probcons_exe = "probcons"
if not probcons_exe:
raise MissingExternalDependencyError(
"Install PROBCONS if you want to use the Bio.Align.Applications wrapper."
)
class ProbconsApplication(unittest.TestCase):
def setUp(self):
self.infile1 = "Fasta/fa01"
self.annotation_outfile = "Fasta/probcons_annot.out"
def tearDown(self):
if os.path.isfile(self.annotation_outfile):
os.remove(self.annotation_outfile)
def test_Probcons_alignment_fasta(self):
"""Round-trip through app and read fasta alignment from stdout."""
cmdline = ProbconsCommandline(probcons_exe, input=self.infile1)
self.assertEqual(str(cmdline), probcons_exe + " Fasta/fa01")
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
stdout, stderr = cmdline()
self.assertTrue(stderr.startswith("\nPROBCONS"))
align = AlignIO.read(StringIO(stdout), "fasta")
records = list(SeqIO.parse(self.infile1, "fasta"))
self.assertEqual(len(records), len(align))
for old, new in zip(records, align):
self.assertEqual(old.id, new.id)
self.assertEqual(
str(new.seq).replace("-", ""), str(old.seq).replace("-", "")
)
def test_Probcons_alignment_clustalw(self):
"""Round-trip through app and read clustalw alignment from stdout."""
cmdline = ProbconsCommandline(probcons_exe)
cmdline.set_parameter("input", "Fasta/fa01")
cmdline.clustalw = True
self.assertEqual(str(cmdline), probcons_exe + " -clustalw Fasta/fa01")
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
stdout, stderr = cmdline()
self.assertTrue(stderr.strip().startswith("PROBCONS"))
align = AlignIO.read(StringIO(stdout), "clustal")
records = list(SeqIO.parse(self.infile1, "fasta"))
self.assertEqual(len(records), len(align))
for old, new in zip(records, align):
self.assertEqual(old.id, new.id)
self.assertEqual(
str(new.seq).replace("-", ""), str(old.seq).replace("-", "")
)
def test_Probcons_complex_commandline(self):
"""Round-trip through app with complex command line and output file."""
cmdline = ProbconsCommandline(probcons_exe, pre=1)
cmdline.set_parameter("input", "Fasta/fa01")
cmdline.consistency = 4
cmdline.set_parameter("--iterative-refinement", 222)
cmdline.set_parameter("a", True)
cmdline.annot = self.annotation_outfile
self.assertEqual(
str(cmdline),
probcons_exe
+ " -c 4 -ir 222 -pre 1 -annot Fasta/probcons_annot.out -a Fasta/fa01",
)
stdout, stderr = cmdline()
self.assertTrue(stderr.startswith("\nPROBCONS"))
self.assertTrue(stdout.startswith(">AK1H_ECOLI/1-378"))
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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