def test_simple_parse(self):
"""Make sure that we can parse all primersearch files.
"""
for file in self.test_files:
h = open(file, "r")
PrimerSearch.read(h)
h.close()
def test_simple_parse(self):
"""Make sure that we can parse all primersearch files.
"""
for file in self.test_files:
h = open(file, "r")
PrimerSearch.read(h)
h.close()
def test_in_depth_normal_parse(self):
"""Make sure the output from a simple primersearch file is correct."""
file = self.test_files[0]
with open(file) as handle:
amp_info = PrimerSearch.read(handle)
self.assertEqual(len(amp_info.amplifiers), 1)
self.assertIn("Test", amp_info.amplifiers)
self.assertEqual(len(amp_info.amplifiers["Test"]), 1)
self.assertEqual(amp_info.amplifiers["Test"][0].length, 218)
self.assertEqual(
amp_info.amplifiers["Test"][0].hit_info, "AC074298 AC074298 \n"
"\tTelomere associated sequence for Arabidopsis thaliana "
"TEL1N from chromosome I, complete sequence.\n"
"\tCCGGTTTCTCTGGTTGAAAA hits forward strand at 114 "
"with 0 mismatches\n"
"\tTCACATTCCCAAATGTAGATCG hits reverse strand at "
"[114] with 0 mismatches")
def test_in_depth_normal_parse(self):
"""Make sure the output from a simple primersearch file is correct."""
file = self.test_files[0]
h = open(file, "r")
amp_info = PrimerSearch.read(h)
h.close()
self.assertEqual(len(amp_info.amplifiers), 1)
self.assertIn("Test", amp_info.amplifiers)
self.assertEqual(len(amp_info.amplifiers["Test"]), 1)
self.assertEqual(amp_info.amplifiers["Test"][0].length, 218)
self.assertEqual(amp_info.amplifiers["Test"][0].hit_info,
"AC074298 AC074298 \n"
"\tTelomere associated sequence for Arabidopsis thaliana "
"TEL1N from chromosome I, complete sequence.\n"
"\tCCGGTTTCTCTGGTTGAAAA hits forward strand at 114 "
"with 0 mismatches\n"
"\tTCACATTCCCAAATGTAGATCG hits reverse strand at "
"[114] with 0 mismatches")
def test_in_depth_normal_parse(self):
"""Make sure the output from a simple primersearch file is correct.
"""
file = self.test_files[0]
h = open(file, "r")
amp_info = PrimerSearch.read(h)
h.close()
assert len(amp_info.amplifiers.keys()) == 1
assert "Test" in amp_info.amplifiers.keys()
assert len(amp_info.amplifiers["Test"]) == 1
assert amp_info.amplifiers["Test"][0].length == 218
assert amp_info.amplifiers["Test"][0].hit_info == \
"AC074298 AC074298 \n" + \
"\tTelomere associated sequence for Arabidopsis thaliana " + \
"TEL1N from chromosome I, complete sequence.\n" + \
"\tCCGGTTTCTCTGGTTGAAAA hits forward strand at 114 with " + \
"0 mismatches\n" + \
"\tTCACATTCCCAAATGTAGATCG hits reverse strand at [114] with " + \
"0 mismatches"
def test_simple_parse(self):
"""Make sure that we can parse all primersearch files."""
for file in self.test_files:
with open(file) as handle:
PrimerSearch.read(handle)