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()