def compare_one(col, cons_aa, aln_size, weights, aa_freqs, pseudo_size):
"""Compare column amino acid frequencies to overall via G-test."""
observed = count_col(col, weights, aa_freqs, pseudo_size)
G = 2 * sum(obsv * math.log(obsv / aa_freqs.get(aa, 0.0))
for aa, obsv in observed.iteritems())
pvalue = chisqprob(G, 19)
return pvalue
def compare_one(col, cons_aa, aln_size, weights, aa_freqs, pseudo_size):
"""Compare column amino acid frequencies to overall via G-test."""
observed = count_col(col, weights, aa_freqs, pseudo_size)
G = 2 * sum(obsv * math.log(obsv / aa_freqs.get(aa, 0.0))
for aa, obsv in observed.iteritems())
pvalue = chisqprob(G, 19)
return pvalue
def compare_cols(fg_col, fg_cons, fg_size, fg_weights, bg_col, bg_cons, bg_size, bg_weights, aa_freqs, pseudo_size):
"""Compare amino acid frequencies between aligned columns via G-test."""
# Calculate the "expected" aa frequencies
bg_counts = count_col(bg_col, bg_weights, aa_freqs, pseudo_size)
expected = {}
for aa in "ACDEFGHIKLMNPQRSTVWY":
# Scale to same size as foreground
expected[aa] = fg_size * (bg_counts[aa] / (bg_size + pseudo_size))
# Calculate the G-value of observed vs. expected
observed = count_col(fg_col, fg_weights)
G = 2 * sum(obsv * math.log(obsv / expected[aa]) for aa, obsv in observed.iteritems())
# 4. Calculate the Chi-squared p-value of G
pvalue = chisqprob(G, 19)
return pvalue
def compare_cols(fg_col, fg_cons, fg_size, fg_weights, bg_col, bg_cons,
bg_size, bg_weights, aa_freqs, pseudo_size):
"""Compare amino acid frequencies between aligned columns via G-test."""
# Calculate the "expected" aa frequencies
bg_counts = count_col(bg_col, bg_weights, aa_freqs, pseudo_size)
expected = {}
for aa in 'ACDEFGHIKLMNPQRSTVWY':
# Scale to same size as foreground
expected[aa] = fg_size * (bg_counts[aa] / (bg_size + pseudo_size))
# Calculate the G-value of observed vs. expected
observed = count_col(fg_col, fg_weights)
G = 2 * sum(obsv * math.log(obsv / expected[aa])
for aa, obsv in observed.iteritems())
# 4. Calculate the Chi-squared p-value of G
pvalue = chisqprob(G, 19)
return pvalue