if __name__ == "__main__": ase = locals().get('ase', None) expr = locals().get('expr', None) if ase is None or expr is None or not np.all(ase.index == expr.index): print("reloading files") expr = pd.read_table('analysis_godot/summary.tsv', **pd_kwargs).dropna(how='all', axis=1) ase = (pd .read_table('analysis_godot/ase_summary_by_read.tsv', **pd_kwargs ) .dropna(how='all', axis=1) .dropna(how='all', axis=0) .select(**sel_startswith(('melXsim', 'simXmel'))) ) chrom_of = get_chroms() males = ('melXsim_cyc14C_rep3', 'simXmel_cyc14C_rep2') on_x = [chrom_of[gene] == 'X' if gene in chrom_of else False for gene in ase.index] is_male = [col.startswith(males) for col in ase.columns] ase.ix[on_x, is_male] = np.nan melXsim_expr = expr.select(**sel_startswith('melXsim')) simXmel_expr = expr.select(**sel_startswith('simXmel')) melXsim_ase = ase.select(**sel_startswith('melXsim')) simXmel_ase = ase.select(**sel_startswith('simXmel')) melXsim_is_expr = (melXsim_expr > EXPR_MIN) simXmel_is_expr = (simXmel_expr > EXPR_MIN) all_is_expr = expr > EXPR_MIN min_per_crossdir = 10
return parser.parse_args() if __name__ == "__main__": filterwarnings("ignore", ".*Covariance of the parameters.*",) filterwarnings("ignore", ".*overflow encountered in exp.*",) #expr = pd.read_table('analysis_godot/summary_fb.tsv', **pd_kwargs).dropna(how='all', axis=1) args = parse_args() ase = (pd .read_table(args.data_to_fit, **pd_kwargs ) .dropna(how='all', axis=1) .dropna(how='all', axis=0) .select(**sel_startswith(('melXsim', 'simXmel'))) ) chrom_of = get_chroms() males = ('melXsim_cyc14C_rep3', 'simXmel_cyc14C_rep2') on_x = [chrom_of[gene] == 'X' if gene in chrom_of else False for gene in ase.index] is_male = [col.startswith(males) for col in ase.columns] ase.ix[on_x, is_male] = np.nan ase = ase.loc[ase.T.count() > len(ase.columns) / 2.0] hours = len(ase) / 1e4 * 1.5 + 2 cluster_args['time'] = '{}:{}:00'.format(int(hours), int((hours % 1)*60)) print("Estimate {} per iteration".format(cluster_args['time'])) #cluster_args['queue'] = fyrd.Queue(user='******', #qtype=fyrd.queue.get_cluster_environment()) print(cluster_args) sys.stdout.flush()