ftab_file = os.path.join('SubsMat', 'protein_count.txt')
with open(ftab_file) as handle:
ftab_prot = FreqTable.read_count(handle)
ctab_file = os.path.join('SubsMat', 'protein_freq.txt')
with open(ctab_file) as handle:
ctab_prot = FreqTable.read_freq(handle)
f.write("Check differences between derived and true frequencies for each\n")
f.write("letter. Differences should be very small\n")
for i in ftab_prot.alphabet.letters:
f.write("%s %f\n" % (i, abs(ftab_prot[i] - ctab_prot[i])))
pickle_file = os.path.join('SubsMat', 'acc_rep_mat.pik')
#Don't want to use text mode on Python 3,
with open(pickle_file, 'rb') as handle:
acc_rep_mat = cPickle.load(handle)
acc_rep_mat = SubsMat.AcceptedReplacementsMatrix(acc_rep_mat)
obs_freq_mat = SubsMat._build_obs_freq_mat(acc_rep_mat)
ftab_prot2 = SubsMat._exp_freq_table_from_obs_freq(obs_freq_mat)
obs_freq_mat.print_mat(f=f, format=" %4.3f")
f.write(
"Diff between supplied and matrix-derived frequencies, should be small\n")
ks = ftab_prot.keys()
ks.sort()
for i in ks:
f.write("%s %.2f\n" % (i, abs(ftab_prot[i] - ftab_prot2[i])))
s = 0.
f.write("Calculating sum of letters for an observed frequency matrix\n")
counts = obs_freq_mat.sum()
keys = counts.keys()
