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python-biopython  1.60
Namespaces | Variables
test_SubsMat.py File Reference

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Namespaces

namespace  test_SubsMat

Variables

 test_SubsMat.f = sys.stdout
tuple test_SubsMat.ftab_file = os.path.join('SubsMat', 'protein_count.txt')
tuple test_SubsMat.ftab_prot = FreqTable.read_count(open(ftab_file))
tuple test_SubsMat.ctab_file = os.path.join('SubsMat', 'protein_freq.txt')
tuple test_SubsMat.ctab_prot = FreqTable.read_freq(open(ctab_file))
tuple test_SubsMat.pickle_file = os.path.join('SubsMat', 'acc_rep_mat.pik')
tuple test_SubsMat.acc_rep_mat = cPickle.load(open(pickle_file, 'rb'))
tuple test_SubsMat.obs_freq_mat = SubsMat._build_obs_freq_mat(acc_rep_mat)
tuple test_SubsMat.ftab_prot2 = SubsMat._exp_freq_table_from_obs_freq(obs_freq_mat)
tuple test_SubsMat.ks = ftab_prot.keys()
int test_SubsMat.s = 0
tuple test_SubsMat.counts = obs_freq_mat.sum()
tuple test_SubsMat.keys = counts.keys()
 test_SubsMat.lo_mat_prot = \
tuple test_SubsMat.mat = SubsMat.SeqMat(getattr(MatrixInfo,i))
tuple test_SubsMat.relative_entropy = lo_mat_prot.calculate_relative_entropy(obs_freq_mat)
tuple test_SubsMat.blosum90 = SubsMat.SeqMat(MatrixInfo.blosum90)
tuple test_SubsMat.blosum30 = SubsMat.SeqMat(MatrixInfo.blosum30)