Python get_ct_dict_metatableの例

コード例 #1

ファイル: compare_events_anno.gtex.py プロジェクト: silvidc/pancanatlas_code_public

        'KICH': 'KICH (N)',
        'KIRC': 'KIRC (N)',
        'KIRP': 'KIRP (N)',
        'LIHC': 'LIHC (N)',
        'LUAD': 'LUAD (N)',
        'PRAD': 'PRAD (N)',
        'READ': 'READ (N)',
        'STAD': 'STAD (N)',
        'THCA': 'THCA (N)',
        'UCEC': 'UCEC (N)',
        'LUSC': 'LUSC (N)'
    }
}

### get cancer type dictionary
(ct_dict, is_tumor_dict) = utils.get_ct_dict_metatable(paths.metadata,
                                                       style=metadata_style)

### create GTex type dictionary
sample_dict = {
    'BLDR': '../annotation/sample_lists_gtex/Bladder.txt',
    'BRST': '../annotation/sample_lists_gtex/Breast.txt',
    'KIDN': '../annotation/sample_lists_gtex/Kidney.txt',
    'LIVR': '../annotation/sample_lists_gtex/Liver.txt',
    'LUNG': '../annotation/sample_lists_gtex/Lung.txt',
    'PRST': '../annotation/sample_lists_gtex/Prostate.txt',
    'SKIN': '../annotation/sample_lists_gtex/Skin.txt',
    'STOM': '../annotation/sample_lists_gtex/Stomach.txt',
    'THYR': '../annotation/sample_lists_gtex/Thyroid.txt',
    'UTER': '../annotation/sample_lists_gtex/Uterus.txt',
    'COLN': '../annotation/sample_lists_gtex/Colon.txt',
    'CELL': '../annotation/sample_lists_gtex/Cells.txt'

コード例 #2

    log_tag = '.log10'

wl_tag = ''
libsize = paths.libsize
if use_whitelist:
    wl_tag = '.whitelisted'
    libsize = paths.libsize_whitelist

pickle_tag = wl_tag + '.G%s' % str(gtex_thresh) + conf_tag
plot_tag = log_tag + pickle_tag

# get lookup table of gene names
lookup = names.get_lookup_complete() 

### get TCGA type dictionary
(ct_dict, is_tumor_dict) = utils.get_ct_dict_metatable(paths.metadata, style='pancan_rerun18')

### create GTex type dictionary
sample_dict = {'ADIP':'../annotation/sample_lists_gtex/Adipose.txt',
               'BLDR':'../annotation/sample_lists_gtex/Bladder.txt',
               'BRAI':'../annotation/sample_lists_gtex/Brain.txt',
               'BRST':'../annotation/sample_lists_gtex/Breast.txt',
               'CERV':'../annotation/sample_lists_gtex/Cervix.txt',
               'COLN':'../annotation/sample_lists_gtex/Colon.txt',
               'ESPH':'../annotation/sample_lists_gtex/Esophagus.txt',
               'KIDN':'../annotation/sample_lists_gtex/Kidney.txt',
               'LIVR':'../annotation/sample_lists_gtex/Liver.txt',
               'LUNG':'../annotation/sample_lists_gtex/Lung.txt',
               'OVRY':'../annotation/sample_lists_gtex/Ovary.txt',
               'PANC':'../annotation/sample_lists_gtex/Pancreas.txt',
               'PRST':'../annotation/sample_lists_gtex/Prostate.txt',