def find_proteins(self, glycopeptide):
out = []
seq = strip_modifications(glycopeptide)
for case in self.sequence_to_model:
if seq in case:
out.append(self.sequence_to_model[case])
return out
def _guess_sites_from_sequence(self, sequence):
prot_seq = str(self.protein)
query_seq = strip_modifications(sequence)
try:
start = prot_seq.index(query_seq)
end = start + len(query_seq)
return PeptideProteinRelation(start, end, self.protein.id,
self.protein.hypothesis_id)
except ValueError:
return None
def get_models(self, glycopeptide):
out = []
seq = strip_modifications(glycopeptide)
if seq in self.peptide_to_protein:
return list(self.peptide_to_protein[seq])
pattern = re.compile(seq)
for case in self.sequence_to_model:
if seq in case:
bounds = pattern.finditer(case)
for match in bounds:
protein_model = self.sequence_to_model[case]
site_models = protein_model.find_sites_in(
match.start(), match.end())
out.append(site_models)
self.peptide_to_protein[seq] = tuple(out)
return out
def convert_to_peptide_dict(glycopeptide, id_tracker):
data = {
"id": glycopeptide.id,
"peptide_sequence": parser.strip_modifications(glycopeptide),
"modifications": []
}
i = 0
# TODO: handle N-terminal and C-terminal modifications
for pos, mods in glycopeptide:
i += 1
if not mods:
continue
else:
mod = mods[0]
if mod.rule.is_a("glycosylation"):
mod_dict = {
"monoisotopic_mass_delta":
glycopeptide.glycan_composition.mass(),
"location":
i,
"name":
"unknown modification",
"params": [
components.UserParam(name='GlycosylationType',
value=str(mod)),
components.UserParam(name='GlycanComposition',
value=str(
glycopeptide.glycan_composition)),
components.UserParam(
name='Formula',
value=formula(glycopeptide.glycan_composition.
total_composition()))
]
}
data['modifications'].append(mod_dict)
else:
mod_dict = {
"monoisotopic_mass_delta": mod.mass,
"location": i,
"name": mod.name,
}
data['modifications'].append(mod_dict)
return data
def convert_to_peptide_dict(glycopeptide, id_tracker):
data = {
"id": glycopeptide.id,
"peptide_sequence": parser.strip_modifications(glycopeptide),
"modifications": [
]
}
i = 0
# TODO: handle N-terminal and C-terminal modifications
for pos, mods in glycopeptide:
i += 1
if not mods:
continue
else:
mod = mods[0]
if mod.rule.is_a("glycosylation"):
mod_dict = {
"monoisotopic_mass_delta": glycopeptide.glycan_composition.mass(),
"location": i,
"name": "unknown modification",
"params": [
components.UserParam(
name='GlycosylationType', value=str(mod)),
components.UserParam(name='GlycanComposition', value=str(
glycopeptide.glycan_composition)),
components.UserParam(name='Formula', value=formula(
glycopeptide.glycan_composition.total_composition()))
]
}
data['modifications'].append(mod_dict)
else:
mod_dict = {
"monoisotopic_mass_delta": mod.mass,
"location": i,
"name": mod.name,
}
data['modifications'].append(mod_dict)
return data
def convert_to_peptide_dict(self, glycopeptide, id_tracker):
data = {
"id": glycopeptide.id,
"peptide_sequence": parser.strip_modifications(glycopeptide),
"modifications": []
}
i = 0
# TODO: handle N-terminal and C-terminal modifications
glycosylation_event_count = len(glycopeptide.convert().glycosylation_manager)
glycosylation_events_handled = 0
for _pos, mods in glycopeptide:
i += 1
if not mods:
continue
else:
mod = mods[0]
if mod.rule.is_a("glycosylation"):
glycosylation_events_handled += 1
is_aggregate_stub = False
mod_params = [
glycosylation_type_to_term(
str(mod.rule.glycosylation_type))
]
if mod.rule.is_core:
mod_params.extend(
self.gnome_resolver.glycan_composition_to_terms(glycopeptide.glycan_composition.clone()))
mass = glycopeptide.glycan_composition.mass()
if glycosylation_event_count == 1:
mod_params.append({
"name": "glycan composition",
"cvRef": "PSI-MS",
"accession": "MS:XXXX14"
})
else:
mod_params.append({
"name": "glycan aggregate",
"cvRef": "PSI-MS",
"accession": "MS:XXXX15"
})
if glycosylation_events_handled > 1:
mass = 0
is_aggregate_stub = True
if not is_aggregate_stub:
mod_params.append({
"accession": 'MS:1000864',
"cvRef": "PSI-MS",
"name": "chemical formula",
"value": formula(glycopeptide.glycan_composition.total_composition()),
})
else:
mod_params.append({
"accession": 'MS:1000864',
"cvRef": "PSI-MS",
"name": "chemical formula",
"value": formula(mod.rule.composition),
})
if mod.rule.is_composition:
mod_params.extend(self.gnome_resolver.glycan_composition_to_terms(mod.rule.glycan.clone()))
mod_params.append({
"name": "glycan composition",
"cvRef": "PSI-MS",
"accession": "MS:XXXX14"
})
else:
mod_params.append({
"name": "glycan structure",
"cvRef": "PSI-MS",
"accession": "MS:XXXXXXX"
})
mass = mod.mass
mod_dict = {
"monoisotopic_mass_delta": mass,
"location": i,
# "name": "unknown modification",
"name": "glycosylation modification",
"params": [components.CVParam(**x) for x in mod_params]
}
data['modifications'].append(mod_dict)
else:
mod_dict = {
"monoisotopic_mass_delta": mod.mass,
"location": i,
"name": mod.name,
}
data['modifications'].append(mod_dict)
return data