def test_add(self):
c = pc.ProgramCaller(config_std)
c_alt = pc.ProgramCaller(config_alt)
c.Add(c_alt)
self.assertEqual(len(c.msa), 5)
self.assertEqual(len(c.tree), 5)
for x in "mafft mergealign muscle another_msa bad_method".split():
self.assertTrue(x in c.msa)
for x in "fasttree raxml iqtree false_method raxml_no_path".split():
self.assertTrue(x in c.tree)
def test_GetMSAMethodCommand(self):
workingDir = "/home/david/WorkingDir/"
c = pc.ProgramCaller(config_std)
# test a method that uses the proposed output filename
cmd, outfn = c.GetMSAMethodCommand("mafft", workingDir + "OG234.fa",
workingDir + "Alignments/OG234.fa",
"OG234_id")
self.assertEqual(
cmd,
"mafft --localpair --maxiterate 1000 --anysymbol /home/david/WorkingDir/OG234.fa > /home/david/WorkingDir/Alignments/OG234.fa 2> /dev/null"
)
cmd, outfn = c.GetMSAMethodCommand("mafft", workingDir + "OGXYZ.fa",
workingDir + "Alignments/OGXXX.fa",
"OGYYY_id")
self.assertEqual(
cmd,
"mafft --localpair --maxiterate 1000 --anysymbol /home/david/WorkingDir/OGXYZ.fa > /home/david/WorkingDir/Alignments/OGXXX.fa 2> /dev/null"
)
# test a method that generates its own output filename based on unique ID - don't actually test what the real output filename is here - need to run it for that
cmd, outfn = c.GetMSAMethodCommand("mergealign",
workingDir + "OG234.fa",
workingDir + "Alignments/OG234.fa",
"OG234_id")
self.assertEqual(
cmd,
"python /home/david/software/MergeAlign/run_mergealign.py /home/david/WorkingDir/OG234.fa"
)
def test_CallTreeMethod(self):
c = pc.ProgramCaller(config_alt)
# Write an input file
infn = output_dir + "Test.fa"
with open(infn, 'wb') as outfile:
outfile.write(">a1\nST\n>b2\nKL\n>c3\nSL\n>d4\nKT")
# test a method that uses the proposed output filename
exp_outfn = output_dir + "OG234.tre"
if os.path.exists(exp_outfn):
os.remove(exp_outfn)
outfn = c.CallTreeMethod("fasttree", infn, exp_outfn, "OGabc_id")
self.assertTrue(outfn != None)
self.assertEqual(outfn, exp_outfn)
expectedTree = "(a1:1.10312,c3:0.00055,(b2:0.00055,d4:1.46340)0.761:1.41871);"
with open(outfn, 'rb') as infile:
tree = infile.read().rstrip()
self.assertEqual(expectedTree, tree)
# test a method that generates its own output filename based on unique ID
exp_outfn = output_dir + "OG234_id.treefile"
if os.path.exists(exp_outfn): os.remove(exp_outfn)
outfn = c.CallTreeMethod("iqtree", infn, output_dir + "OG234.tre",
"OG234_id")
self.assertEqual(outfn, exp_outfn)
# with open(outfn, 'rb') as infile: tree = infile.read().rstrip()
expectedTree = ete2.Tree(
"(a1:0.7475350209,(b2:0.0000026604,c3:1.2318876921):1.279964,d4:0.0000022111);"
)
actualTree = ete2.Tree(outfn)
for n in expectedTree:
x = (actualTree & n.name).dist
self.assertLess(
abs(x - n.dist) / n.dist, 0.3,
(n.dist, (actualTree & n.name).dist))
def test_CallMSAMethod(self):
c = pc.ProgramCaller(config_alt)
# Write an input file
infn = output_dir + "Test.fa"
with open(infn, 'wb') as outfile:
outfile.write(">a1\nST\n>b2\nKL\n>c3\nSL\n>d4\nKT\n")
# test a method that uses the proposed output filename
exp_outfn = output_dir + "OG234.fa"
if os.path.exists(exp_outfn):
os.remove(exp_outfn)
outfn = c.CallMSAMethod("mafft", infn, exp_outfn, "OGabc_id")
self.assertTrue(outfn != None)
self.assertEqual(outfn, exp_outfn)
self.assertTrue(filecmp.cmp(
infn, outfn)) # Alignment should be same as input
# test a method that generates its own output filename based on input filename
exp_outfn = output_dir + "MergeAlign_alignment_Test.fa"
if os.path.exists(exp_outfn):
os.remove(outfn)
outfn = c.CallMSAMethod("mergealign", infn,
output_dir + "Alignments/OG234.fa", "OG234_id")
self.assertEqual(outfn, exp_outfn)
self.assertTrue(
filecmp.cmp(
baseDir +
"ExpectedOutput/ProgramCaller/MergeAlign_alignment_Test.fa",
outfn))
def test_space(self):
with captured_output() as (out, err):
c = pc.ProgramCaller(config_space)
self.assertTrue(len(c.msa) == 1)
self.assertTrue("mergealign" in c.msa)
self.assertFalse("maf ft" in c.msa)
output = out.getvalue().strip()
expected_out = """WARNING: Incorrecty formatted configuration file entry: maf ft\nNo space is allowed in name: 'maf ft'"""
self.assertEqual(output, expected_out)
error = err.getvalue().strip()
self.assertEqual(error, "")
def test_malformatted_json(self):
with captured_output() as (out, err):
c = pc.ProgramCaller(config_bad_json)
self.assertTrue(len(c.msa) == 0)
self.assertTrue(len(c.tree) == 0)
output = out.getvalue().strip()
expected_out = """WARNING: Incorrecty formatted configuration file /home/david/workspace/git/OrthoFinder/Tests/Input/ConfigFiles/configure_bad_json.json
File is not in .json format. No user-confgurable multiple sequence alignment or tree inference methods have been added."""
self.assertEqual(output, expected_out)
error = err.getvalue().strip()
self.assertEqual(error, "")
def test_TestTreeMethod(self):
c = pc.ProgramCaller(config_alt)
# test a method that won't work
self.assertFalse(c.TestTreeMethod(output_dir, "false_method"))
# test a method that ses the proposed output filename
self.assertTrue(c.TestTreeMethod(output_dir, "fasttree"))
# test a method that generates its own output filename based on unique ID
self.assertTrue(c.TestTreeMethod(output_dir, "iqtree"))
self.assertRaises(Exception, c.TestTreeMethod, output_dir, "made_up")
# test a program not in path
self.assertFalse(c.TestTreeMethod(output_dir, "raxml_no_path"))
def test_normal_construct(self):
c = pc.ProgramCaller(config_std)
methods_msa = "mafft mergealign muscle another_msa".split()
methods_trees = "fasttree raxml iqtree".split()
msa = c.ListMSAMethods()
self.assertEqual(len(msa), len(methods_msa))
for m in methods_msa:
self.assertTrue(m in msa, m)
trees = c.ListTreeMethods()
self.assertEqual(len(trees), len(methods_trees))
for m in methods_trees:
self.assertTrue(m in trees, m)
c = pc.ProgramCaller(config_alt)
methods_msa = "mafft mergealign bad_method".split()
methods_trees = "fasttree iqtree false_method raxml_no_path".split()
msa = c.ListMSAMethods()
self.assertEqual(len(msa), len(methods_msa))
for m in methods_msa:
self.assertTrue(m in msa, m)
trees = c.ListTreeMethods()
self.assertEqual(len(trees), len(methods_trees))
for m in methods_trees:
self.assertTrue(m in trees, m)
