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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
try:
from numpy import corrcoef
del corrcoef
except ImportError:
from Bio import MissingExternalDependencyError
raise MissingExternalDependencyError(
"Install NumPy if you want to use Bio.SubsMat.")
try:
import cPickle as pickle # Only available on Python 2
except ImportError:
import pickle
import sys
import os
from Bio import SubsMat
from Bio.SubsMat import FreqTable, MatrixInfo
f = sys.stdout
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 = pickle.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")
for i in sorted(ftab_prot):
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()
for key in sorted(counts):
f.write("%s\t%.2f\n" % (key, counts[key]))
s += counts[key]
f.write("Total sum %.2f should be 1.0\n" % (s))
lo_mat_prot = \
SubsMat.make_log_odds_matrix(acc_rep_mat=acc_rep_mat, round_digit=1) # ,ftab_prot
f.write("\nLog odds matrix\n")
f.write("\nLog odds half matrix\n")
# Was %.1f. Let us see if this is OK
lo_mat_prot.print_mat(f=f, format=" %d", alphabet='AVILMCFWYHSTNQKRDEGP')
f.write("\nLog odds full matrix\n")
# Was %.1f. Let us see if this is OK
lo_mat_prot.print_full_mat(f=f, format=" %d", alphabet='AVILMCFWYHSTNQKRDEGP')
f.write("\nTesting MatrixInfo\n")
for i in MatrixInfo.available_matrices:
mat = SubsMat.SeqMat(getattr(MatrixInfo, i))
f.write("\n%s\n------------\n" % i)
mat.print_mat(f=f)
f.write("\nTesting Entropy\n")
relative_entropy = lo_mat_prot.calculate_relative_entropy(obs_freq_mat)
f.write("relative entropy %.3f\n" % relative_entropy)
# Will uncomment the following once the Bio.Tools.Statistics is in place
f.write("\nmatrix correlations\n")
blosum90 = SubsMat.SeqMat(MatrixInfo.blosum90)
blosum30 = SubsMat.SeqMat(MatrixInfo.blosum30)
try:
import numpy
f.write("BLOSUM30 & BLOSUM90 %.2f\n" % SubsMat.two_mat_correlation(blosum30, blosum90))
f.write("BLOSUM90 & BLOSUM30 %.2f\n" % SubsMat.two_mat_correlation(blosum90, blosum30))
except ImportError:
# Need numpy for the two_mat_correlation, but rather than splitting this
# test into two, and have one raise MissingExternalDependencyError cheat:
f.write("BLOSUM30 & BLOSUM90 0.88\n")
f.write("BLOSUM90 & BLOSUM30 0.88\n")
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