def test_properties(self):
"""Test setting options via properties."""
input_file = self.copy_and_mark_for_cleanup("Fasta/f002")
cline = XXmotifCommandline(outdir=self.out_dir, seqfile=input_file)
cline.revcomp = True
cline.pseudo = 20
cline.startmotif = "ACGGGT"
self.standard_test_procedure(cline)
def test_properties(self):
"""Test setting options via properties."""
input_file = self.copy_and_mark_for_cleanup("Fasta/f002")
cline = XXmotifCommandline(outdir=self.out_dir,
seqfile=input_file)
cline.revcomp = True
cline.pseudo = 20
cline.startmotif = "ACGGGT"
self.standard_test_procedure(cline)
def test_output_directory_with_space(self):
"""Test an output directory containing a space."""
temp_out_dir = "xxmotif test"
input_file = self.copy_and_mark_for_cleanup("Fasta/f002")
try:
cline = XXmotifCommandline(outdir=temp_out_dir, seqfile=input_file)
except ValueError:
pass
else:
self.fail("expected ValueError")
def test_invalid_format(self):
"""Test an input file in an invalid format."""
input_file = self.copy_and_mark_for_cleanup("Medline/pubmed_result1.txt")
cline = XXmotifCommandline(outdir = self.out_dir,
seqfile = input_file)
try:
stdout, stderr = cline()
except ApplicationError, err:
self.assertEqual(err.returncode, 255)
def test_empty_file(self):
"""Test a non-existing input file."""
input_file = "does_not_exist.fasta"
self.assertFalse(os.path.isfile(input_file))
cline = XXmotifCommandline(outdir=self.out_dir, seqfile=input_file)
try:
stdout, stderr = cline()
except ApplicationError, err:
self.assertEqual(err.returncode, 255)
def test_input_filename_with_space(self):
"""Test an input filename containing a space."""
input_file = "temp horses.fasta"
handle = open(input_file, "w")
SeqIO.write(SeqIO.parse("Phylip/hennigian.phy", "phylip"), handle,
"fasta")
handle.close()
cline = XXmotifCommandline(outdir=self.out_dir, seqfile=input_file)
self.add_file_to_clean(input_file)
self.standard_test_procedure(cline)
def test_large_fasta_file(self):
"""Test a large fasta input file."""
input_file = "temp_b_nuc.fasta"
handle = open(input_file, "w")
records = list(SeqIO.parse("NBRF/B_nuc.pir", "pir"))
SeqIO.write(records, handle, "fasta")
handle.close()
del handle, records
cline = XXmotifCommandline(outdir=self.out_dir, seqfile=input_file)
self.add_file_to_clean(input_file)
self.standard_test_procedure(cline)
def test_fasta_one_sequence(self):
"""Test a fasta input file containing only one sequence."""
input_file = "seq.fasta"
handle = open(input_file, "w")
record = list(SeqIO.parse("Registry/seqs.fasta", "fasta"))[0]
SeqIO.write(record, handle, "fasta")
handle.close()
del handle, record
cline = XXmotifCommandline(outdir=self.out_dir, seqfile=input_file)
self.add_file_to_clean(input_file)
self.standard_test_procedure(cline)
