def make_df(self, tax_id = False):
hdr = ['enzyme', 'substrate', 'isoforms',
'residue_type', 'residue_offset', 'modification',
'sources', 'references']
self.df = pd.DataFrame(
[dm.get_line() for dm in self],
columns = hdr
).astype(
{
'enzyme': 'category',
'substrate': 'category',
'isoforms': 'category',
'residue_type': 'category',
'residue_offset': 'int32',
'modification': 'category',
}
)
self.df['enzyme_genesymbol'] = pd.Series([
(
mapping.map_name0(
u,
id_type = 'uniprot',
target_id_type = 'genesymbol',
ncbi_tax_id = self.ncbi_tax_id,
) or ''
)
for u in self.df.enzyme
])
self.df['substrate_genesymbol'] = pd.Series([
(
mapping.map_name0(
u,
id_type = 'uniprot',
target_id_type = 'genesymbol',
ncbi_tax_id = self.ncbi_tax_id,
) or ''
)
for u in self.df.substrate
])
hdr.insert(2, 'enzyme_genesymbol')
hdr.insert(3, 'substrate_genesymbol')
self.df = self.df.loc[:,hdr]
if tax_id:
self.df['ncbi_tax_id'] = [self.ncbi_tax_id] * self.df.shape[0]
def build_gene(self):
self.gene = set()
for entity in self._entities:
# we add the components of the complexes to the protein data
# frame; I don't know if it's necessary but does not harm I guess
if hasattr(entity, 'components'):
components = entity.components
else:
components = (entity, )
for comp in components:
name = mapping.map_name0(comp, 'uniprot', 'genesymbol')
ensembl_genes = mapping.map_name(comp, 'uniprot', 'ensembl')
for ensembl in ensembl_genes:
self.gene.add(
CellPhoneDBGene(
gene_name=name,
uniprot=comp,
hgnc_symbol=name,
ensembl=ensembl,
))
def stoichiometry_str_genesymbols(self):
return ';'.join(
itertools.chain(*(((mapping.map_name0(
uniprot,
'uniprot',
'genesymbol',
) or uniprot), ) * cnt for uniprot, cnt in sorted(
iteritems(self.components),
key=lambda comp_cnt: comp_cnt[0],
))))
def get_id_name(entity):
id_ = entity.__str__()
name = (id_ if 'COMPLEX' in id_ else mapping.map_name0(
id_,
'uniprot',
'uniprot-entry',
))
return id_, name
def build_protein(self):
integrins = annot.db.annots['Integrins']
self.cpdb_protein = set()
for entity in self._entities:
# we add the components of the complexes to the protein data
# frame; I don't know if it's necessary but does not harm I guess
if hasattr(entity, 'components'):
components = entity.components
else:
components = (entity,)
for comp in components:
classes = self.intercell.classes_by_entity(comp)
self.cpdb_protein.add(
CellPhoneDBProtein(
uniprot = comp.__str__(),
protein_name = mapping.map_name0(
comp,
'uniprot',
'uniprot-entry',
),
transmembrane = 'transmembrane' in classes,
peripheral = 'cell_surface' in classes,
secreted = 'secreted' in classes,
secreted_desc = '',
secreted_highlight = '',
receptor = 'receptor' in classes,
receptor_desc = '',
integrin = comp in integrins,
other = '',
other_desc = '',
tags = '',
tags_reason = '',
tags_description = '',
)
)
def genesymbols(self):
return sorted(
(mapping.map_name0(uniprot, 'uniprot', 'genesymbol') or uniprot)
for uniprot in self.components.keys())
