def test_tostring(self):
for seq in self.simple_sequences:
self.assertEqual(
seq, parser.tostring(parser.parse(seq, labels=uppercase)))
self.assertEqual(
seq,
parser.tostring(
parser.parse(seq, True, True, labels=uppercase), False))
def generate_Yion(Ytype, aa_mass, ion_maxcharge, ion_type, labels, temp):
str_seq = parser.tostring(temp, False)
for m in range(ion_maxcharge):
if "Y" in ion_type:
yield Ion(seq=temp, charge=m + 1, ion_type="Y",
mz=mass.fast_mass2(str_seq, charge=m + 1, aa_mass=aa_mass, labels=labels),
fragment_number=int(Ytype[1:]) + 1)
def generate_byion(aa_mass, b_stop_at, ion_maxcharge, ion_type, labels, seq_len, temp, y_stop_at, b_selected, y_selected):
for s in range(seq_len):
if not (s + 1) == 1:
for m in range(ion_maxcharge):
for ion in ion_type:
if ion == "y":
position = seq_len - s - 1
if y_stop_at > -1:
if position <= y_stop_at:
continue
if y_selected:
if position in y_selected:
seq = temp[position:]
str_seq = parser.tostring(seq, False)
# print(str_seq)
yield Ion(seq=temp, ion_type=ion, charge=m + 1,
mz=mass.fast_mass2(str_seq, ion_type=ion, charge=m + 1, aa_mass=aa_mass,
labels=labels), fragment_number=s + 1)
else:
seq = temp[position:]
str_seq = parser.tostring(seq, False)
# print(str_seq)
yield Ion(seq=temp, ion_type=ion, charge=m + 1,
mz=mass.fast_mass2(str_seq, ion_type=ion, charge=m + 1, aa_mass=aa_mass,
labels=labels), fragment_number=s + 1)
elif ion == "b":
position = s + 1
if position == seq_len:
continue
if b_stop_at > -1:
if position > b_stop_at:
continue
if b_selected:
if s in b_selected:
seq = temp[:position]
str_seq = parser.tostring(seq, False)
# print(str_seq)
yield Ion(seq=temp, ion_type=ion, charge=m + 1,
mz=mass.fast_mass2(str_seq, ion_type=ion, charge=m + 1, aa_mass=aa_mass,
labels=labels), fragment_number=s + 1)
else:
seq = temp[:position]
str_seq = parser.tostring(seq, False)
# print(str_seq)
yield Ion(seq=temp, ion_type=ion, charge=m + 1,
mz=mass.fast_mass2(str_seq, ion_type=ion, charge=m + 1, aa_mass=aa_mass,
labels=labels), fragment_number=s + 1)
def fragmenting(i,
rec,
ms,
mv,
query_unique,
protein_id,
unique_q3=None,
y=None):
labels, aa_mass, seq = prepare_libraries(i['_protein']['_sequence'],
static=ms,
variable=mv)
seq_len = len(seq)
result = []
msMap = {m['label']: m['m_label'] for m in ms}
for f in generate_fragments(seq[:], static=ms, variable=mv):
# print(f)
new_seq = parser.tostring(f, False)
print('Current: ' + new_seq)
precursor_mz = mass.fast_mass2(new_seq,
charge=i['_precursor_charge'],
aa_mass=aa_mass,
labels=labels)
variable = ''
for r in i['_rt']:
for ion in fragments_by(aa_mass,
i['_charge'],
i['_protein']['_ion_type'],
labels,
seq_len,
f,
mv,
Ytype=y,
b_stop_at=i['_b_stop_at'],
y_stop_at=i['_y_stop_at'],
by_static=i['_by_run'],
b_selected=i['_b_selected'],
y_selected=i['_y_selected']):
create_row(f, i, ion, msMap, mv, precursor_mz, query_unique, r,
rec, result, seq, seq_len, unique_q3, variable,
protein_id)
return result, query_unique