def __init__(self, identifier, ptms=None):
'''
identifier : str
UniProt AC of the protein.
ptms : list
List 3 element tuples, containing
residue name, number and the PTM type (e.g. phosphorylation).
'''
self.id = identifier
self.ptms = []
if ptms is not None:
for name, number, typ in ptms:
res = intera.Residue(number, name, identifier)
ptm = intera.Ptm(identifier, residue=res, typ=typ)
def translate_ptm(self, ptm):
tptms = self.translate_site(ptm.protein, ptm.residue.name,
ptm.residue.number, ptm.residue.isoform,
ptm.typ)
result = []
if self.target in tptms:
for x in tptms[self.target]:
se = self.get_seq(x[0])
if (se is None or x[1] not in se.isof) and self.strict:
continue
res = intera.Residue(x[3], x[2], x[0], isoform=x[1])
start, end, region = (se.get_region(x[3], isoform=x[1]) if
se is not None and x[1] in se.isof else
(None, None, None))
mot = intera.Motif(x[0],
start=start,
end=end,
instance=region,
isoform=x[1])
ptm = intera.Ptm(x[0],
motif=mot,
residue=res,
typ=x[5],
isoform=x[1],
source=ptm.sources)
result.append(ptm)
return result
def _process(self, p):
# human leukocyte antigenes result a result an
# extremely high number of combinations
if (not p['kinase'] or (isinstance(p['substrate'], common.basestring)
and p['substrate'].startswith('HLA'))):
return
if not isinstance(p['kinase'], list):
p['kinase'] = [p['kinase']]
kinase_ups = mapping.map_names(
p['kinase'],
self.enzyme_id_type,
'uniprot',
ncbi_tax_id=self.ncbi_tax_id,
)
substrate_ups_all = set([])
for sub_id_type in (self.substrate_id_types[self.input_method.lower()]
if self.input_is(self.substrate_id_types,
'__contains__') else
[self.substrate_id_type]):
if type(sub_id_type) is tuple:
sub_id_type, sub_id_attr = sub_id_type
else:
sub_id_attr = 'substrate'
substrate_ups_all.update(
set(
mapping.map_name(
p[sub_id_attr],
sub_id_type,
'uniprot',
self.ncbi_tax_id,
)))
# looking up sequences in all isoforms:
substrate_ups = []
for s in substrate_ups_all:
if 'substrate_isoform' in p and p['substrate_isoform']:
substrate_ups.append((s, p['substrate_isoform']))
else:
se = self.get_seq(s)
if se is None:
continue
for isof in se.isoforms():
if p['instance'] is not None:
if se.match(p['instance'],
p['start'],
p['end'],
isoform=isof):
substrate_ups.append((s, isof))
else:
if se.match(p['resaa'], p['resnum'], isoform=isof):
substrate_ups.append((s, isof))
if self.trace:
if p['substrate'] not in self.sub_ambig:
self.sub_ambig[p['substrate']] = substrate_ups
for k in p['kinase']:
if k not in self.kin_ambig:
self.kin_ambig[k] = kinase_ups
# generating report on non matching substrates
if len(substrate_ups) == 0:
for s in substrate_ups_all:
se = self.get_seq(s[0])
if se is None:
continue
nomatch.append(
(s[0], s[1], ((p['substrate_refseq']
if 'substrate_refseq' in p else ''), s,
p['instance'],
se.get(p['start'], p['end']))))
# adding kinase-substrate interactions
for k in kinase_ups:
for s in substrate_ups:
if (not self.allow_mixed_organisms
and (self.get_taxon(k) != self.ncbi_tax_id
or self.get_taxon(s[0]) != self.ncbi_tax_id)):
continue
se = self.get_seq(s[0])
if se is None:
continue
res = intera.Residue(p['resnum'],
p['resaa'],
s[0],
isoform=s[1])
if p['instance'] is None:
reg = se.get_region(p['resnum'],
p['start'],
p['end'],
isoform=s[1])
if reg is not None:
p['instance'] = reg[2]
p['start'] = reg[0]
p['end'] = reg[1]
if 'typ' not in p:
p['typ'] = 'phosphorylation'
mot = intera.Motif(s[0],
p['start'],
p['end'],
instance=p['instance'],
isoform=s[1])
ptm = intera.Ptm(s[0],
motif=mot,
residue=res,
typ=p['typ'],
source=[self.name],
isoform=s[1])
dom = intera.Domain(protein=k)
if 'references' not in p:
p['references'] = []
dommot = intera.DomainMotif(domain=dom,
ptm=ptm,
sources=[self.name],
refs=p['references'])
if self.input_is('mimp'):
dommot.mimp_sources = ';'.split(p['databases'])
dommot.npmid = p['npmid']
elif self.input_is('phosphonetworks'):
dommot.pnetw_score = p['score']
elif self.input_is('dbptm'):
dommot.dbptm_sources = [p['source']]
yield dommot