def get_subtype_reference_alignment_entropy(region, subtype='B', VERBOSE=0,
refname='HXB2',
type='nuc'):
'''Get the entropy of a large subtype reference alignment'''
import numpy as np
fn = get_subtype_reference_alignment_entropy_filename(region,
subtype=subtype,
refname=refname,
type=type,
VERBOSE=VERBOSE)
return np.load(fn)
def get_subtype_reference_alignment_entropy(region,
subtype='B',
VERBOSE=0,
refname='HXB2',
type='nuc'):
'''Get the entropy of a large subtype reference alignment'''
import numpy as np
fn = get_subtype_reference_alignment_entropy_filename(region,
subtype=subtype,
refname=refname,
type=type,
VERBOSE=VERBOSE)
return np.load(fn)
VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Compute entropy'
if alitype == 'nuc':
alphabet = alpha[:4]
else:
alphabet = alphaa[:-3]
S = get_ali_entropy(ali, alpha=alphabet, VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Store to file'
fn_out = get_subtype_reference_alignment_entropy_filename(region,
subtype=subtype,
refname=refname,
type=alitype,
VERBOSE=VERBOSE)
S.dump(fn_out)
else:
if VERBOSE >= 2:
print 'Get entropy from file'
S = get_subtype_reference_alignment_entropy(region,
subtype=subtype,
refname=refname,
type=alitype,
VERBOSE=VERBOSE)
Ss[region] = S
VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Compute entropy'
if alitype == 'nuc':
alphabet = alpha[:4]
else:
alphabet = alphaa[:-3]
S = get_ali_entropy(ali, alpha=alphabet, VERBOSE=VERBOSE)
if VERBOSE >= 2:
print 'Store to file'
fn_out = get_subtype_reference_alignment_entropy_filename(
region,
subtype=subtype,
refname=refname,
type=alitype,
VERBOSE=VERBOSE)
S.dump(fn_out)
else:
if VERBOSE >= 2:
print 'Get entropy from file'
S = get_subtype_reference_alignment_entropy(region,
subtype=subtype,
refname=refname,
type=alitype,
VERBOSE=VERBOSE)
Ss[region] = S
