def test_dnal(self):
"""Call dnal, and do a trivial check on its output."""
Wise.align(["dnal"], ("seq1.fna", "seq2.fna"),
kbyte=100000,
dry_run=True)
self.assert_(sys.stdout.getvalue().startswith(
"dnal -kbyte 100000 seq1.fna seq2.fna"))
def test_psw(self):
"""Call psw, and do a trivial check on its output."""
Wise.align(["psw"], ("seq1.faa", "seq2.faa"), dry_run=True, kbyte=4)
#If test output is redirected to a file, the wrapper adds -quiet
output = sys.stdout.getvalue().replace(" -quiet ", " ")
self.assertTrue(output.startswith("psw -kbyte 4 seq1.faa seq2.faa"),
output[:200])
def test_dnal(self):
"""Call dnal, and do a trivial check on its output."""
Wise.align(["dnal"], ("seq1.fna", "seq2.fna"),
kbyte=100000,
dry_run=True)
#If test output is redirected to a file, the wrapper adds -quiet
output = sys.stdout.getvalue().replace(" -quiet ", " ")
self.assertTrue(
output.startswith("dnal -kbyte 100000 seq1.fna seq2.fna"),
output[:200])
def test_align(self):
"""Call dnal with optional arguments, and do a trivial check on the output."""
temp_file = Wise.align(
["dnal"],
("Wise/human_114_g01_exons.fna_01",
"Wise/human_114_g02_exons.fna_01"),
kbyte=100000,
force_type="DNA",
quiet=True,
)
line = temp_file.readline().rstrip()
if line == "Score 114":
# Wise 2.4.1 includes a score line, even in quiet mode, ignore this
line = temp_file.readline().rstrip()
if (line ==
"ENSG00000172135 AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCC"
):
# This is what we expect from wise 2.2.0 (and earlier)
pass
elif (line ==
"ENSG00000172135 AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAG-TGGGGTCC"
):
# This is what we expect from wise 2.4.1
pass
else:
# Bad!
self.fail(line)
def align(pair, match=_SCORE_MATCH, mismatch=_SCORE_MISMATCH, gap=_SCORE_GAP_START, extension=_SCORE_GAP_EXTENSION, **keywds):
cmdline = _build_dnal_cmdline(match, mismatch, gap, extension)
temp_file = Wise.align(cmdline, pair, **keywds)
try:
return Statistics(temp_file.name, match, mismatch, gap, extension)
except AttributeError:
try:
keywds['dry_run']
return None
except KeyError:
raise
def align(pair, scores=None, gap_start=None, gap_extension=None, *args, **keywds):
cmdline = _CMDLINE_PSW[:]
if scores:
cmdline.extend((_OPTION_SCORES, scores))
if gap_start:
cmdline.extend((_OPTION_GAP_START, str(gap_start)))
if gap_extension:
cmdline.extend((_OPTION_GAP_EXTENSION, str(gap_extension)))
temp_file = Wise.align(cmdline, pair, *args, **keywds)
return parse(temp_file)
def align(pair, match=_SCORE_MATCH, mismatch=_SCORE_MISMATCH, gap=_SCORE_GAP_START, extension=_SCORE_GAP_EXTENSION, **keywds):
cmdline = _build_dnal_cmdline(match, mismatch, gap, extension)
temp_file = Wise.align(cmdline, pair, **keywds)
try:
return Statistics(temp_file.name, match, mismatch, gap, extension)
except AttributeError:
try:
keywds['dry_run']
return None
except KeyError:
raise
def align(pair, match=_SCORE_MATCH, mismatch=_SCORE_MISMATCH, gap=_SCORE_GAP_START, extension=_SCORE_GAP_EXTENSION, **keywds):
"""Align a pair of DNA files using dnal and calculate the statistics of the alignment."""
cmdline = _build_dnal_cmdline(match, mismatch, gap, extension)
temp_file = Wise.align(cmdline, pair, **keywds)
try:
return Statistics(temp_file.name, match, mismatch, gap, extension)
except AttributeError:
try:
keywds['dry_run']
return None
except KeyError:
raise
def align(pair, match=_SCORE_MATCH, mismatch=_SCORE_MISMATCH, gap=_SCORE_GAP_START, extension=_SCORE_GAP_EXTENSION, **keywds):
"""Align a pair of DNA files using dnal and calculate the statistics of the alignment."""
cmdline = _build_dnal_cmdline(match, mismatch, gap, extension)
temp_file = Wise.align(cmdline, pair, **keywds)
try:
return Statistics(temp_file.name, match, mismatch, gap, extension)
except AttributeError:
try:
keywds['dry_run']
return None
except KeyError:
raise
def align(pair,
scores=None,
gap_start=None,
gap_extension=None,
*args, **keywds):
cmdline = _CMDLINE_PSW[:]
if scores:
cmdline.extend((_OPTION_SCORES, scores))
if gap_start:
cmdline.extend((_OPTION_GAP_START, str(gap_start)))
if gap_extension:
cmdline.extend((_OPTION_GAP_EXTENSION, str(gap_extension)))
temp_file = Wise.align(cmdline, pair, *args, **keywds)
return parse(temp_file)
def test_align(self):
"""Call dnal with optional arguments, and do a trivial check on the output."""
temp_file = Wise.align(["dnal"], ("Wise/human_114_g01_exons.fna_01", "Wise/human_114_g02_exons.fna_01"), kbyte=100000, force_type="DNA", quiet=True)
line = temp_file.readline().rstrip()
if line == "Score 114" :
#Wise 2.4.1 includes a score line, even in quiet mode, ignore this
line = temp_file.readline().rstrip()
if line == "ENSG00000172135 AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCC" :
#This is what we expect from wise 2.2.0 (and earlier)
pass
elif line == "ENSG00000172135 AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAG-TGGGGTCC" :
#This is what we expect from wise 2.4.1
pass
else :
#Bad!
self.assert_(False, line)
def test_psw(self):
"""Call psw, and do a trivial check on its output."""
Wise.align(["psw"], ("seq1.faa", "seq2.faa"), dry_run=True, kbyte=4)
self.assert_(sys.stdout.getvalue().startswith("psw -kbyte 4 seq1.faa seq2.faa"))
def test_dnal(self):
"""Call dnal, and do a trivial check on its output."""
Wise.align(["dnal"], ("seq1.fna", "seq2.fna"), kbyte=100000, dry_run=True)
self.assert_(sys.stdout.getvalue().startswith("dnal -kbyte 100000 seq1.fna seq2.fna"))
def test_psw(self):
"""Call psw, and do a trivial check on its output."""
Wise.align(["psw"], ("seq1.faa", "seq2.faa"), dry_run=True, kbyte=4)
# If test output is redirected to a file, the wrapper adds -quiet
output = sys.stdout.getvalue().replace(" -quiet ", " ")
self.assertTrue(output.startswith("psw -kbyte 4 seq1.faa seq2.faa"), output[:200])
def test_dnal(self):
"""Call dnal, and do a trivial check on its output."""
Wise.align(["dnal"], ("seq1.fna", "seq2.fna"), kbyte=100000, dry_run=True)
# If test output is redirected to a file, the wrapper adds -quiet
output = sys.stdout.getvalue().replace(" -quiet ", " ")
self.assertTrue(output.startswith("dnal -kbyte 100000 seq1.fna seq2.fna"), output[:200])
def test_psw(self):
"""Call psw, and do a trivial check on its output."""
Wise.align(["psw"], ("seq1.faa", "seq2.faa"), dry_run=True, kbyte=4)
self.assert_(
sys.stdout.getvalue().startswith("psw -kbyte 4 seq1.faa seq2.faa"))