Source code for indra.databases.context_client

from __future__ import absolute_import, print_function, unicode_literals
from builtins import dict, str
from copy import copy
from indra.databases import cbio_client
# Python 2
try:
    basestring
# Python 3
except:
    basestring = str


[docs]def get_protein_expression(gene_names, cell_types): """Return the protein expression levels of genes in cell types. Parameters ---------- gene_names : list HGNC gene symbols for which expression levels are queried. cell_types : list List of cell type names in which expression levels are queried. The cell type names follow the CCLE database conventions. Example: LOXIMVI_SKIN, BT20_BREAST Returns ------- res : dict[dict[float]] A dictionary keyed by cell line, which contains another dictionary that is keyed by gene name, with estimated protein amounts as values. """ A = 0.2438361 B = 3.0957627 mrna_amounts = cbio_client.get_ccle_mrna(gene_names, cell_types) protein_amounts = copy(mrna_amounts) for cell_type in cell_types: amounts = mrna_amounts.get(cell_type) if amounts is None: continue for gene_name, amount in amounts.items(): if amount is not None: protein_amount = 10**(A * amount + B) protein_amounts[cell_type][gene_name] = protein_amount return protein_amounts
[docs]def get_mutations(gene_names, cell_types): """Return protein amino acid changes in given genes and cell types. Parameters ---------- gene_names : list HGNC gene symbols for which mutations are queried. cell_types : list List of cell type names in which mutations are queried. The cell type names follow the CCLE database conventions. Example: LOXIMVI_SKIN, BT20_BREAST Returns ------- res : dict[dict[list]] A dictionary keyed by cell line, which contains another dictionary that is keyed by gene name, with a list of amino acid substitutions as values. """ mutations = cbio_client.get_ccle_mutations(gene_names, cell_types) return mutations