/
20080225e.py
85 lines (79 loc) · 3.06 KB
/
20080225e.py
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"""Given a rate matrix, check the detailed balance equations for reversibility.
"""
from StringIO import StringIO
import math
import numpy as np
from SnippetUtil import HandlingError
import MatrixUtil
import RateMatrix
import Form
import FormOut
def get_form():
"""
@return: the body of a form
"""
# define the default rate matrix
dictionary_rate_matrix = RateMatrix.get_sample_codon_rate_matrix()
labels = list(sorted(set(a for a, b in dictionary_rate_matrix)))
R = MatrixUtil.dict_to_row_major(dictionary_rate_matrix, labels, labels)
R = np.array(R)
form_objects = [
Form.Matrix('matrix', 'rate matrix',
R, MatrixUtil.assert_rate_matrix)]
return form_objects
def get_form_out():
return FormOut.Report()
def get_response_content(fs):
# read the matrix from the form data
R = fs.matrix
# get the stationary distribution of the rate matrix
try:
v = RateMatrix.get_stationary_distribution(R.tolist())
except RateMatrix.RateMatrixError as e:
msg = 'error calculating the stationary distribution: ' + str(e)
raise HandlingError(msg)
# for each pair of entries, check the detailed balance equation
table_rows = []
for i, pi_i in enumerate(v):
for j, pi_j in enumerate(v):
r_ij = R[i][j]
r_ji = R[j][i]
if pi_i*r_ij != pi_j*r_ji:
row = []
row.append(abs(math.log(pi_i * r_ij) - math.log(pi_j * r_ji)))
row.extend([pi_i, pi_j, r_ij, r_ji])
table_rows.append(row)
# write some stuff
out = StringIO()
if table_rows:
# get the detailed balance html rows
detailed_balance_rows = []
for row in reversed(list(sorted(table_rows))):
detailed_balance_rows.append(''.join('<td>' + str(value) + '</td>' for value in row))
# get the header row
header_entries = []
header_entries.append('abs(log(π<sub>i</sub>r<sub>ij</sub>)-log(π<sub>j</sub>r<sub>ji</sub>))')
header_entries.append('π<sub>i</sub>')
header_entries.append('π<sub>j</sub>')
header_entries.append('r<sub>ij</sub>')
header_entries.append('r<sub>ji</sub>')
header_row = ''.join('<th>%s</th>' % entry for entry in header_entries)
# show detailed balance equation results
print >> out, '<p>'
print >> out, 'This table shows each state pair for which the detailed balance equation is not satisfied exactly.'
print >> out, '</p>'
print >> out, '<html>'
print >> out, '<body>'
print >> out, '<table>'
print >> out, '<tr>' + header_row + '</tr>'
for row in detailed_balance_rows:
print >> out, '<tr>' + row + '</tr>'
print >> out, '</table>'
print >> out, '</body>'
print >> out, '</html>'
else:
print >> out, '<html><body>'
print >> out, 'All detailed balance equations are satisfied for this rate matrix.'
print >> out, '</body></html>'
# return the response
return out.getvalue()