raise MissingExternalDependencyError( "Install NumPy if you want to use Bio.SubsMat.") import cPickle 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 = 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(
# 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. import cPickle 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') ftab_prot = FreqTable.read_count(open(ftab_file)) ctab_file = os.path.join('SubsMat', 'protein_freq.txt') ctab_prot = FreqTable.read_freq(open(ctab_file)) 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, acc_rep_mat = cPickle.load(open(pickle_file, 'rb')) 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()
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")
import cPickle 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') ftab_prot = FreqTable.read_count(open(ftab_file)) ctab_file = os.path.join('SubsMat', 'protein_freq.txt') ctab_prot = FreqTable.read_freq(open(ctab_file)) 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') acc_rep_mat = cPickle.load(open(pickle_file)) 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.