def test_real_redundant_discoverer(self):
"""
When there aren't redundancy data_discoverer
"""
path_ = path.join(redundants_dir,
"redundant_accessions_discoverer.xls")
p = proteomic_xls.discoverer_parser()
a_d = dict(fileName=path_)
self.assertRaises(proteomic_xls.Same_Accession, p.parse, **a_d)
def test_file_source_store(self):
"""
testing the original seq storage
"""
p = proteomic_xls.discoverer_parser(mode=True)
for f in self.files:
try:
p.parse(path.join(discoverer_dir, f))
except proteomic_xls.EmptyCell:
pass
self.assertListEqual([path.join(discoverer_dir, f)\
for f in self.files], p.sources)
def test_proteins(self):
"""
proteins occurrence during parsing the five file
"""
p = proteomic_xls.discoverer_parser()
msg = "{0}: predicted {1} != counted {2}"
for i, f in enumerate(self.files):
try:
p.parse(path.join(discoverer_dir, f))
except proteomic_xls.EmptyCell:
pass
for acc, occs in self.prots:
self.assertEqual(occs[i], p.proteins[acc], msg.format(acc, occs[i], p.proteins[acc]))
def test_spectral_count_false_discoverer(self):
"""
Using a data_discoverer file with peptides no-distinct,
the frequencies must be equal to one.
"""
chase2 = path.join(redundants_dir, "redundant_discoverer.xls")
p = proteomic_xls.discoverer_parser()
try:
p.parse(chase2)
except proteomic_xls.EmptyCell:
pass
finally:
for acc, pepts in p.peptides.iteritems():
for seq, occ in pepts.iteritems():
self.assertEqual(occ, 1)
def test_peptides_protpept_nored(self):
"""
peptides occurrence during parsing the five file
Spectral count False
"""
p = proteomic_xls.discoverer_parser()
for i, f in enumerate(self.files):
try:
p.parse(path.join(discoverer_dir, f))
except proteomic_xls.EmptyCell:
pass
for acc, pepts in self.pepts:
for seq, occs_nr, occs_r in pepts:
self.assertEqual(occs_nr[i], p.peptides[acc][seq], "{0} - {1}:{2} aspected {3} != retrived {4}".format(
f, acc, seq, occs_nr[i], p.peptides[acc][seq]))
def test_wrong_peptides_discoverer(self):
path_ = path.join(wrong_pepts_dir, "wrong_pepts_discoverer.xls")
p = proteomic_xls.discoverer_parser()
a_d = dict(fileName=path_)
self.assertRaises(data_input.bad_format_peptide, p.parse, **a_d)