def test_conversion_and_reverse(self):
args = get_args(["-in"] + dna_data_fas +
["-r", "teste", "-c"],
unittest=True)
triseq_arg_check(args)
def test_reverse_concatenate(self):
args = get_args(["-in", concatenated_small_phy[0],
"-r", concatenated_small_par[0],
"-of", "fasta",
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
exp = []
data = []
for fl in sorted([x for x in os.listdir(".")
if x.startswith("BaseConc")]):
with open(fl) as fh:
data.append(sorted([x.rstrip().lower()
for x in fh.readlines()]))
os.remove(fl)
for fl in dna_data_fas:
with open(fl) as fh:
exp.append(sorted([x.rstrip().lower()
for x in fh.readlines()]))
self.assertEqual(exp, data)
def teste_consensus_single_file(self):
args = get_args(["-in", "teste"] +
["--consensus-single-file", "-c", "-quiet"],
unittest=True)
triseq_arg_check(args)
def teste_consensus_single_file(self):
args = get_args(["-in", "teste"] +
["--consensus-single-file", "-c", "-quiet"],
unittest=True)
triseq_arg_check(args)
def test_reverse_concatenate(self):
args = get_args([
"-in", concatenated_small_phy[0], "-r", concatenated_small_par[0],
"-of", "fasta", "-quiet"
],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
exp = []
data = []
for fl in sorted(
[x for x in os.listdir(".") if x.startswith("BaseConc")]):
with open(fl) as fh:
data.append(
sorted([x.rstrip().lower() for x in fh.readlines()]))
os.remove(fl)
for fl in dna_data_fas:
with open(fl) as fh:
exp.append(sorted([x.rstrip().lower()
for x in fh.readlines()]))
self.assertEqual(exp, data)
def test_gap_coding_warning(self):
args = get_args(["-in"] + dna_data_fas +
["-of", "fasta", "nexus", "-c", "-quiet",
"--code-gaps"],
unittest=True)
triseq_arg_check(args)
def test_gap_coding_warning(self):
args = get_args(
["-in"] + dna_data_fas +
["-of", "fasta", "nexus", "-c", "-quiet", "--code-gaps"],
unittest=True)
triseq_arg_check(args)
def test_code_gaps(self):
args = get_args(["-in"] + dna_data_fas + [
"--code-gaps", "-o",
join(output_dir, "teste"), "-of", "nexus", "-quiet"
],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
def teste_no_output_concatenation(self):
args = get_args(["-in"] + dna_data_fas + ["-p", "teste", "-quiet"],
unittest=True)
with self.assertRaises(SystemExit) as cm:
triseq_arg_check(args)
self.assertEqual(cm.exception.code, 1)
def test_code_gaps(self):
args = get_args(["-in"] + dna_data_fas +
["--code-gaps",
"-o", join(output_dir, "teste"),
"-of", "nexus",
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
def teste_consensus_outformats(self):
args = get_args(["-in", "teste"] + ["--consensus", "IUPAC", "-quiet"],
unittest=True)
with self.assertRaises(SystemExit) as cm:
triseq_arg_check(args)
self.assertEqual(cm.exception.code, 1)
def teste_no_ima2_params(self):
args = get_args(["-in"] + dna_data_fas +
["-o", "teste", "-of", "ima2", "-quiet"],
unittest=True)
with self.assertRaises(SystemExit) as cm:
triseq_arg_check(args)
self.assertEqual(cm.exception.code, 1)
def teste_consensus_outformats(self):
args = get_args(["-in", "teste"] +
["--consensus", "IUPAC", "-quiet"],
unittest=True)
with self.assertRaises(SystemExit) as cm:
triseq_arg_check(args)
self.assertEqual(cm.exception.code, 1)
def teste_single_concatenation_with_zorro(self):
args = get_args(["-in", "teste"] +
["-o", "teste", "-z", "teste", "-quiet"],
unittest=True)
with self.assertRaises(SystemExit) as cm:
triseq_arg_check(args)
self.assertEqual(cm.exception.code, 1)
def teste_single_concatenation_with_zorro(self):
args = get_args(["-in", "teste"] +
["-o", "teste", "-z", "teste", "-quiet"],
unittest=True)
with self.assertRaises(SystemExit) as cm:
triseq_arg_check(args)
self.assertEqual(cm.exception.code, 1)
def teste_no_output_concatenation(self):
args = get_args(["-in"] + dna_data_fas +
["-p", "teste", "-quiet"],
unittest=True)
with self.assertRaises(SystemExit) as cm:
triseq_arg_check(args)
self.assertEqual(cm.exception.code, 1)
def test_gap_coding_outformat(self):
args = get_args(["-in"] + dna_data_fas +
["-of", "fasta", "-c", "-quiet", "--code-gaps"],
unittest=True)
with self.assertRaises(SystemExit) as cm:
triseq_arg_check(args)
self.assertEqual(cm.exception.code, 1)
def teste_no_ima2_params(self):
args = get_args(["-in"] + dna_data_fas +
["-o", "teste", "-of", "ima2", "-quiet"],
unittest=True)
with self.assertRaises(SystemExit) as cm:
triseq_arg_check(args)
self.assertEqual(cm.exception.code, 1)
def test_get_taxa(self):
args = get_args(["-in"] + dna_data_fas + ["--get-taxa", "-quiet"],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
self.assertTrue(os.path.exists("Taxa_list.csv"))
os.remove("Taxa_list.csv")
def test_informative_filter(self):
args = get_args(["-in"] + dna_data_fas +
["--informative-filter", "1", "2",
"-o", join(output_dir, "teste"),
"-of", "fasta",
"-quiet"])
triseq_arg_check(args)
main_parser(args, args.infile)
self.assertTrue(os.path.exists(join(output_dir, "teste.fas")))
def test_get_taxa(self):
args = get_args(["-in"] + dna_data_fas +
["--get-taxa",
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
self.assertTrue(os.path.exists("Taxa_list.csv"))
os.remove("Taxa_list.csv")
def test_interleave(self):
args = get_args(["-in"] + dna_data_fas +
["--interleave",
"-o", join(output_dir, "teste"),
"-of", "fasta",
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
self.assertTrue(os.path.exists(join(output_dir, "teste.fas")))
def test_gap_coding_outformat(self):
args = get_args(["-in"] + dna_data_fas +
["-of", "fasta", "-c", "-quiet",
"--code-gaps"],
unittest=True)
with self.assertRaises(SystemExit) as cm:
triseq_arg_check(args)
self.assertEqual(cm.exception.code, 1)
def test_missing_filter_prop_val(self):
args = get_args(["-in"] + dna_data_fas +
["--missing-filter", "0.1", "0.5",
"-o", join(output_dir, "teste"),
"-of", "fasta",
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
self.assertTrue(os.path.exists(join(output_dir, "teste.fas")))
def test_convert_raxml2nex(self):
args = get_args(["-p", concatenated_small_parNex[0],
"-o", join(output_dir, "test"),
"-quiet"])
triseq_arg_check(args)
main_parser(args, args.infile)
with open(concatenated_small_par[0]) as fh1, \
open(join(output_dir, "test.part.File")) as fh2:
self.assertEqual(fh1.read(), fh2.read().replace("LG", "DNA"))
def test_convert_raxml2nex(self):
args = get_args(["-p", concatenated_small_parNex[0],
"-o", join(output_dir, "test"),
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
with open(concatenated_small_par[0]) as fh1, \
open(join(output_dir, "test.part.File")) as fh2:
self.assertEqual(fh1.read(), fh2.read().replace("LG", "DNA"))
def test_exclude_taxa(self):
args = get_args(["-in"] + dna_data_fas +
["--exclude-taxa", "spa",
"-o", join(output_dir, "teste"),
"-of", "fasta",
"-quiet"])
triseq_arg_check(args)
main_parser(args, args.infile)
self.assertTrue(os.path.exists(join(output_dir, "teste.fas")))
def test_ima2_output(self):
args = get_args(["-in"] + dna_data_fas + [
"--ima2-params", ima2_pop_file, "(1,2):3)4:5", "IS", "1", "-o",
join(output_dir, "teste"), "-of", "ima2", "-quiet"
],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
self.assertTrue(os.path.exists(join(output_dir, "teste.txt")))
def test_missing_filter_prop_val(self):
args = get_args(["-in"] + dna_data_fas + [
"--missing-filter", "0.1", "0.5", "-o",
join(output_dir, "teste"), "-of", "fasta", "-quiet"
],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
self.assertTrue(os.path.exists(join(output_dir, "teste.fas")))
def test_interleave(self):
args = get_args(["-in"] + dna_data_fas + [
"--interleave", "-o",
join(output_dir, "teste"), "-of", "fasta", "-quiet"
],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
self.assertTrue(os.path.exists(join(output_dir, "teste.fas")))
def test_grep_taxa(self):
args = get_args(["-in"] + dna_data_fas + [
"-grep", "spa", "-o",
join(output_dir, "teste"), "-of", "fasta", "-quiet"
],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
with open(join(output_dir, "teste.fas")) as fh:
self.assertEqual(fh.read().count("spa"), 1)
def test_ima2_output(self):
args = get_args(["-in"] + dna_data_fas +
["--ima2-params", ima2_pop_file, "(1,2):3)4:5", "IS",
"1",
"-o", join(output_dir, "teste"),
"-of", "ima2",
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
self.assertTrue(os.path.exists(join(output_dir, "teste.txt")))
def test_simple_concatenation(self):
args = get_args(["-in"] + dna_data_fas +
["-of", "fasta",
"-o", join(output_dir, "teste"),
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
with open(join(data_path, "BaseConcatenation.fas")) as fh1, \
open(join(output_dir, "teste.fas")) as fh2:
self.assertEqual(sorted(fh1.readlines()), sorted(fh2.readlines()))
def test_grep_taxa(self):
args = get_args(["-in"] + dna_data_fas +
["-grep", "spa",
"-o", join(output_dir, "teste"),
"-of", "fasta",
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
with open(join(output_dir, "teste.fas")) as fh:
self.assertEqual(fh.read().count("spa"), 1)
def test_select_alignments(self):
args = get_args(["-in"] + dna_data_fas + ["-s", "spa", "-quiet"],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
fls = sorted(os.listdir("Taxa_selection"))
shutil.rmtree("Taxa_selection")
self.assertEqual(fls, ["BaseConc1.fas", "BaseConc7.fas"])
def test_simple_concatenation(self):
args = get_args(["-in"] + dna_data_fas +
["-of", "fasta",
"-o", join(output_dir, "teste"),
"-quiet"])
triseq_arg_check(args)
main_parser(args, args.infile)
with open(join(data_path, "BaseConcatenation.fas")) as fh1, \
open(join(output_dir, "teste.fas")) as fh2:
self.assertEqual(fh1.read(), fh2.read())
def test_consensus_singlefile(self):
args = get_args(["-in"] + dna_data_fas + [
"--consensus", "Soft mask", "--consensus-single-file", "-of",
"fasta", "-c", "-quiet"
],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
self.assertTrue(os.path.exists(join("consensus", "consensus.fas")))
shutil.rmtree("consensus")
def test_collapse(self):
args = get_args(["-in"] + dna_data_fas + [
"--collapse", "-o",
join(output_dir, "teste"), "-of", "fasta", "-quiet"
],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
fls = sorted(os.listdir(output_dir))
self.assertEqual(fls, ['teste.fas', 'teste.haplotypes'])
def test_collapse(self):
args = get_args(["-in"] + dna_data_fas +
["--collapse",
"-o", join(output_dir, "teste"),
"-of", "fasta",
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
fls = sorted(os.listdir(output_dir))
self.assertEqual(fls, ['teste.fas', 'teste.haplotypes'])
def test_select_alignments(self):
args = get_args(["-in"] + dna_data_fas +
["-s", "spa",
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
fls = sorted(os.listdir("Taxa_selection"))
shutil.rmtree("Taxa_selection")
self.assertEqual(fls, ["BaseConc1.fas", "BaseConc7.fas"])
def test_convert_par2raxml(self):
args = get_args([
"-p", concatenated_small_par[0], "-o",
join(output_dir, "test"), "-quiet"
],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
with open(concatenated_small_parNex[0]) as fh1, \
open(join(output_dir, "test.charset")) as fh2:
self.assertEqual(fh1.read(), fh2.read())
def test_consensus(self):
args = get_args(["-in", dna_data_fas[0],
"--consensus", "Soft mask",
"-of", "fasta",
"-c",
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
with open("BaseConc1.fas") as fh:
self.assertTrue(fh.read().startswith(">consensus"))
os.remove("BaseConc1.fas")
def test_simple_conversion(self):
args = get_args(
["-in", dna_data_fas[0], "-of", "fasta", "-c", "-quiet"],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
with open(join(data_path, "BaseConc1.fas")) as fh1, \
open("BaseConc1.fas") as fh2:
self.assertEqual(fh1.read().rstrip().lower(),
fh2.read().rstrip().lower())
os.remove("BaseConc1.fas")
def test_consensus_singlefile(self):
args = get_args(["-in"] + dna_data_fas +
["--consensus", "Soft mask",
"--consensus-single-file",
"-of", "fasta",
"-c",
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
self.assertTrue(os.path.exists(join("consensus","consensus.fas")))
shutil.rmtree("consensus")
def test_consensus(self):
args = get_args([
"-in", dna_data_fas[0], "--consensus", "Soft mask", "-of", "fasta",
"-c", "-quiet"
],
unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
with open("BaseConc1.fas") as fh:
self.assertTrue(fh.read().startswith(">consensus"))
os.remove("BaseConc1.fas")
def test_simple_conversion(self):
args = get_args(["-in", dna_data_fas[0],
"-of", "fasta",
"-c",
"-quiet"], unittest=True)
triseq_arg_check(args)
main_parser(args, args.infile)
with open(join(data_path, "BaseConc1.fas")) as fh1, \
open("BaseConc1.fas") as fh2:
self.assertEqual(fh1.read().rstrip().lower(),
fh2.read().rstrip().lower())
os.remove("BaseConc1.fas")
def test_conversion_and_reverse(self):
args = get_args(["-in"] + dna_data_fas + ["-r", "teste", "-c"],
unittest=True)
triseq_arg_check(args)