def get_ali_entropy_syn(alim, positions=None, alpha=alpha[:5], VERBOSE=0):
'''Get entropy of alignment at some positions'''
from collections import defaultdict
from hivwholeseq.utils.sequence import translate_with_gaps as translate
if len(ali[0]) % 3:
raise ValueError('The alignment length is not a multiple of 3')
if positions is None:
positions = np.arange(len(ali[0]) // 3)
# The data structure is a nested dict by position and amino acid
S = {}
# Iterate over codons
for pos in positions:
if VERBOSE >= 3:
print pos
asub = alim[:, pos * 3: (pos + 1) * 3]
aacount = defaultdict(lambda: defaultdict(int))
for cod in asub:
cod = ''.join(cod)
aacount[translate(cod)][cod] += 1
Spos = {}
for aa, codd in aacount.iteritems():
af = np.array(codd.values(), float)
af /= af.sum()
Spos[aa] = get_entropy(af)
S[pos] = Spos
return S
def get_ali_entropy_syn(alim, positions=None, alpha=alpha[:5], VERBOSE=0):
'''Get entropy of alignment at some positions'''
from collections import defaultdict
from hivwholeseq.utils.sequence import translate_with_gaps as translate
if len(ali[0]) % 3:
raise ValueError('The alignment length is not a multiple of 3')
if positions is None:
positions = np.arange(len(ali[0]) // 3)
# The data structure is a nested dict by position and amino acid
S = {}
# Iterate over codons
for pos in positions:
if VERBOSE >= 3:
print pos
asub = alim[:, pos * 3:(pos + 1) * 3]
aacount = defaultdict(lambda: defaultdict(int))
for cod in asub:
cod = ''.join(cod)
aacount[translate(cod)][cod] += 1
Spos = {}
for aa, codd in aacount.iteritems():
af = np.array(codd.values(), float)
af /= af.sum()
Spos[aa] = get_entropy(af)
S[pos] = Spos
return S
def get_ali_entropy(ali, positions=None, alpha=alpha[:5], VERBOSE=0):
'''Get entropy of alignment at some positions
Parameters:
- alpha: alphabet for the sequences, defaults to ACGT-.
'''
if positions is None:
positions = np.arange(len(ali[0]))
afs = np.zeros((len(alpha), len(positions)))
for i, pos in enumerate(positions):
af = np.zeros(len(alpha), float)
col = np.fromstring(ali[:, pos], 'S1')
for ia, nuc in enumerate(alpha):
af[ia] = (col == nuc).sum()
af /= af.sum()
afs[:, i] = af
S = get_entropy(afs)
return S
def get_ali_entropy(ali, positions=None, alpha=alpha[:5], VERBOSE=0):
'''Get entropy of alignment at some positions
Parameters:
- alpha: alphabet for the sequences, defaults to ACGT-.
'''
if positions is None:
positions = np.arange(len(ali[0]))
afs = np.zeros((len(alpha), len(positions)))
for i, pos in enumerate(positions):
af = np.zeros(len(alpha), float)
col = np.fromstring(ali[:, pos], 'S1')
for ia, nuc in enumerate(alpha):
af[ia] = (col == nuc).sum()
af /= af.sum()
afs[:, i] = af
S = get_entropy(afs)
return S
