def read_ccle_variants(gene_names):
"""Return genetic variants reported by CCLE (via web service)"""
cell_lines_db = [cl + '_SKIN' for cl in cell_lines]
nons = cbio_client.get_ccle_mutations(gene_names, cell_lines_db,
'nonsense')
miss = cbio_client.get_ccle_mutations(gene_names, cell_lines_db,
'missense')
tmp = copy.deepcopy(nons)
for cell_line, content in tmp.items():
for gene, muts in content.items():
if not muts:
nons[cell_line].pop(gene, None)
tmp = copy.deepcopy(miss)
for cell_line, content in tmp.items():
for gene, muts in content.items():
if not muts:
miss[cell_line].pop(gene, None)
continue
# Check for usable AA substitution
grouped_muts = []
for mut in muts:
match = re.match('([A-Z])(\d+)([A-Z])', mut)
if not match:
continue
groups = match.groups()
if len(groups) != 3:
continue
grouped_muts.append(groups)
miss[cell_line][gene] = grouped_muts
variants = {}
variants['missense'] = miss
variants['nonsense'] = nons
return variants
def test_get_ccle_mutations():
muts = cbio_client.get_ccle_mutations(['BRAF', 'AKT1'],
['LOXIMVI_SKIN', 'A101D_SKIN'])
assert len([x for x in muts]) == 2
assert 'V600E' in muts['LOXIMVI_SKIN']['BRAF']
assert 'V600E' in muts['A101D_SKIN']['BRAF']
assert 'I208V' in muts['LOXIMVI_SKIN']['BRAF']
assert 'I208V' not in muts['A101D_SKIN']['BRAF']
assert len(muts['LOXIMVI_SKIN']['AKT1']) == 0
assert len(muts['A101D_SKIN']['AKT1']) == 0
def test_get_ccle_mutations():
muts = cbio_client.get_ccle_mutations(['BRAF', 'AKT1'],
['LOXIMVI_SKIN', 'A101D_SKIN'])
assert len([x for x in muts]) == 2
assert 'V600E' in muts['LOXIMVI_SKIN']['BRAF']
assert 'V600E' in muts['A101D_SKIN']['BRAF']
assert 'I208V' in muts['LOXIMVI_SKIN']['BRAF']
assert 'I208V' not in muts['A101D_SKIN']['BRAF']
assert len(muts['LOXIMVI_SKIN']['AKT1']) == 0
assert len(muts['A101D_SKIN']['AKT1']) == 0
def get_ccle_mutations():
"""Get CCLE mutations
returns the amino acid changes for a given list of genes and cell lines
"""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
gene_list = body.get('gene_list')
cell_lines = body.get('cell_lines')
mutations = cbio_client.get_ccle_mutations(gene_list, cell_lines)
res = {'mutations': mutations}
return res
def get_ccle_mutations():
"""Get CCLE mutations
returns the amino acid changes for a given list of genes and cell lines
"""
if request.method == 'OPTIONS':
return {}
response = request.body.read().decode('utf-8')
body = json.loads(response)
gene_list = body.get('gene_list')
cell_lines = body.get('cell_lines')
mutations = cbio_client.get_ccle_mutations(gene_list, cell_lines)
res = {'mutations': mutations}
return res
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
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
def post(self):
"""Get CCLE mutations
Parameters
----------
gene_list : list[str]
A list of HGNC gene symbols to get mutations in
cell_lines : list[str]
A list of CCLE cell line names to get mutations for.
Returns
-------
mutations : dict
The result from cBioPortal as a dict in the format
{cell_line : {gene : [mutation1, mutation2, ...] }}
"""
args = request.json
gene_list = args.get('gene_list')
cell_lines = args.get('cell_lines')
mutations = cbio_client.get_ccle_mutations(gene_list, cell_lines)
res = {'mutations': mutations}
return res