Esempi in Python per CCLE_Info.split_ccle_name

Esempio n. 1

File: gen_expression_data.py Progetto: lrgr-events/technica-data-fall2018

def restrict_to_cell_lines(df, cell_lines):
    new_colname = [CCLE_Info.split_ccle_name(n)[0] for n in list(df.columns)]
    df.columns = new_colname
    df_truncated = df[['Description'] + cell_lines]
    df_truncated = df_truncated.rename(columns={'Description': 'Gene'})
    df_truncated = df_truncated.set_index('Gene')
    return df_truncated.T

Esempio n. 2

File: gen_cell_lines.py Progetto: lrgr-events/technica-data-fall2018

def expression_cell(fp):
    df = pd.read_csv(fp, sep='\t', header=0, skiprows=range(0, 2))
    cells = list(df.columns)
    cells.remove('Name')
    cells.remove('Description')
    cell_lines = [CCLE_Info.split_ccle_name(n)[0] for n in cells]
    return set(cell_lines)

Esempio n. 3

File: tests.py Progetto: lrgr-events/technica-data-fall2018

 def test_CCLE_info(self):
     ccle_info = CCLE_Info('../data/raw/CCLE_metadata.csv')
     self.assertEqual(ccle_info.split_ccle_name('NIHOVCAR3_OVARY'), ('NIHOVCAR3','OVARY'))
     self.assertEqual(ccle_info.broad_id_2_ccle_name('ACH-000001'), 'NIHOVCAR3')
     self.assertEqual(ccle_info.ccle_name_2_broad_id('NIHOVCAR3'),'ACH-000001' )