multi_dendrix.white_and_blacklisting

multi_dendrix.white_and_blacklisting(patient_wlst=None, patient_blst=None, gene_wlst=None, gene_blst=None)

Reconciles the different white- and blacklists provided as input into Multi-Dendrix.

Parameters:

• patient_wlst (string) – File location of patients to be included in analyzed mutation data.
• patient_blst (string) – File location of patients to be excluded in analyzed mutation data.
• gene_wlst (string) – File location of patients to be included in analyzed mutation data.
• gene_blst (string) – File location of patients to be excluded in analyzed mutation data.

Returns:

• gene2include (dictionary): mapping of genes to whether they should be included in the analyzed mutation data.
• patient2include (dictionary): mapping of patients to whether they should be included in the analyzed mutation data.

Examples:

(For brevity, examples are for patient white- and blacklists only)

Patient whitelisting only:

>>> patient_wlst = 'patient.wlst'
>>> open(patient_wlst).readlines()
["TCGA-01", "TCGA-02", "TCGA-03"]
>>> white_and_blacklisting(patient_wlst)
(defaultdict(<function <lambda>>, {}), {"TCGA-01", "TCGA-02", "TCGA-03"})

Conflicting patient white- and blacklists (whitelist has final word):

>>> patient_blst = 'patient.blst'
>>> open(patient_wlst).readlines()
["TCGA-02", "TCGA-04"]
>>> white_and_blacklisting(patient_wlst)
(defaultdict(<function <lambda>>, {}), {"TCGA-01", "TCGA-02", "TCGA-03"})

See also: load_mutation_data(), load_mutation_data_w_cutoff().