def test_bad_format_real_protpept(self):
"""
Should fail with format no protpept using
wrong protpept analysis files
"""
p = proteomic_xls.sequest_protpept_parser()
self.match_format_parser(p.parse, onlypept_dir)
self.match_format_parser(p.parse, discoverer_dir)
def test_wrong_peptides_protpept(self):
"""
When protpept file has wrong peptides
"""
path_ = path.join(wrong_pepts_dir, "wrong_pepts_protpept.xls")
p = proteomic_xls.sequest_protpept_parser()
a_d = dict(fileName=path_)
self.assertRaises(data_input.bad_format_peptide, p.parse, **a_d)
def test_real_redundant_protpept(self):
"""
When there aren't redundancy in proptpept
"""
path_ = path.join(redundants_dir,
"redundant_accessions_protpept.xls")
p = proteomic_xls.sequest_protpept_parser()
a_d = dict(fileName=path_)
self.assertRaises(proteomic_xls.Same_Accession, p.parse, **a_d)
def test_file_source_store_pp(self):
"""
testing the original seq storage
"""
p = proteomic_xls.sequest_protpept_parser(mode=True)
for f in self.files:
try:
p.parse(path.join(protpept_dir, f))
except proteomic_xls.EmptyCell:
pass
self.assertListEqual([path.join(protpept_dir, f) for f in self.files],
p.sources)
def test_proteins_protpept(self):
"""
proteins occurrence during parsing the five file
"""
p = proteomic_xls.sequest_protpept_parser()
for i, f in enumerate(self.files):
try:
p.parse(path.join(protpept_dir, f))
except proteomic_xls.EmptyCell:
pass
for acc, occs in self.prots:
self.assertEqual(occs[i], p.proteins[acc])
def test_peptides_protpept_red(self):
"""
peptides occurrence during parsing the five file
Spectral Count True
"""
p = proteomic_xls.sequest_protpept_parser(mode=True)
for i, f in enumerate(self.files):
try:
p.parse(path.join(protpept_dir, f))
except proteomic_xls.EmptyCell:
pass
for acc, pepts in self.pepts:
for seq, occs_nr, occs_r in pepts:
self.assertEqual(occs_r[i], p.peptides[acc][seq], "%d, %s, %s" %(i, acc, seq))
def test_spectral_count_false_proppept(self):
"""
Using a protpept file with peptides no-distinct,
the frequencies must be equal to one.
"""
chase1 = path.join(redundants_dir, "redundant_protpept.xls")
#assert(os.path.isfile(chase1))
p = proteomic_xls.sequest_protpept_parser()
try:
p.parse(chase1)
except proteomic_xls.EmptyCell:
pass
finally:
for acc, pepts in p.peptides.iteritems():
for seq, occ in pepts.iteritems():
self.assertEqual(occ, 1)