def get_ccle_mutations(gene_list, cell_lines, mutation_type=None):
    """Return a dict of mutations in given genes and cell lines from CCLE.

    This is a specialized call to get_mutations tailored to CCLE cell lines.

    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.
    mutation_type : Optional[str]
        The type of mutation to filter to.
        mutation_type can be one of: missense, nonsense, frame_shift_ins,
        frame_shift_del, splice_site

    Returns
    -------
    mutations : dict
        The result from cBioPortal as a dict in the format
        {cell_line : {gene : [mutation1, mutation2, ...] }}

        Example:
        {'LOXIMVI_SKIN': {'BRAF': ['V600E', 'I208V']},
        'SKMEL30_SKIN': {'BRAF': ['D287H', 'E275K']}}
    """
    mutations = {cl: {g: [] for g in gene_list} for cl in cell_lines}
    for cell_line in cell_lines:
        mutations_cl = get_mutations(ccle_study, gene_list,
                                     mutation_type=mutation_type,
                                     case_id=cell_line)
        for gene, aa_change in zip(mutations_cl['gene_symbol'],
                                   mutations_cl['amino_acid_change']):
            aa_change = str(aa_change)
            mutations[cell_line][gene].append(aa_change)
    return mutations
def get_ccle_mutations ( gene_list , cell_lines , mutation_type = None ) : mutations = { cl : { g : [ ] for g in gene_list } for cl in cell_lines } for cell_line in cell_lines : mutations_cl = get_mutations ( ccle_study , gene_list , mutation_type = mutation_type , case_id = cell_line ) for gene , aa_change in zip ( mutations_cl [ 'gene_symbol' ] , mutations_cl [ 'amino_acid_change' ] ) : aa_change = str ( aa_change ) mutations [ cell_line ] [ gene ] . append ( aa_change ) return mutations
Return a dict of mutations in given genes and cell lines from CCLE.

    This is a specialized call to get_mutations tailored to CCLE cell lines.

    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.
    mutation_type : Optional[str]
        The type of mutation to filter to.
        mutation_type can be one of: missense, nonsense, frame_shift_ins,
        frame_shift_del, splice_site

    Returns
    -------
    mutations : dict
        The result from cBioPortal as a dict in the format
        {cell_line : {gene : [mutation1, mutation2, ...] }}

        Example:
        {'LOXIMVI_SKIN': {'BRAF': ['V600E', 'I208V']},
        'SKMEL30_SKIN': {'BRAF': ['D287H', 'E275K']}}