Back to index

python-biopython  1.60
Variables
test_SubsMat Namespace Reference

Variables

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

Variable Documentation

tuple test_SubsMat.acc_rep_mat = cPickle.load(open(pickle_file, 'rb'))

Definition at line 31 of file test_SubsMat.py.

tuple test_SubsMat.blosum30 = SubsMat.SeqMat(MatrixInfo.blosum30)

Definition at line 75 of file test_SubsMat.py.

tuple test_SubsMat.blosum90 = SubsMat.SeqMat(MatrixInfo.blosum90)

Definition at line 74 of file test_SubsMat.py.

tuple test_SubsMat.counts = obs_freq_mat.sum()

Definition at line 46 of file test_SubsMat.py.

tuple test_SubsMat.ctab_file = os.path.join('SubsMat', 'protein_freq.txt')

Definition at line 22 of file test_SubsMat.py.

tuple test_SubsMat.ctab_prot = FreqTable.read_freq(open(ctab_file))

Definition at line 23 of file test_SubsMat.py.

test_SubsMat.f = sys.stdout

Definition at line 19 of file test_SubsMat.py.

tuple test_SubsMat.ftab_file = os.path.join('SubsMat', 'protein_count.txt')

Definition at line 20 of file test_SubsMat.py.

tuple test_SubsMat.ftab_prot = FreqTable.read_count(open(ftab_file))

Definition at line 21 of file test_SubsMat.py.

tuple test_SubsMat.ftab_prot2 = SubsMat._exp_freq_table_from_obs_freq(obs_freq_mat)

Definition at line 34 of file test_SubsMat.py.

tuple test_SubsMat.keys = counts.keys()

Definition at line 47 of file test_SubsMat.py.

tuple test_SubsMat.ks = ftab_prot.keys()

Definition at line 39 of file test_SubsMat.py.

Definition at line 53 of file test_SubsMat.py.

tuple test_SubsMat.mat = SubsMat.SeqMat(getattr(MatrixInfo,i))

Definition at line 65 of file test_SubsMat.py.

tuple test_SubsMat.obs_freq_mat = SubsMat._build_obs_freq_mat(acc_rep_mat)

Definition at line 33 of file test_SubsMat.py.

tuple test_SubsMat.pickle_file = os.path.join('SubsMat', 'acc_rep_mat.pik')

Definition at line 29 of file test_SubsMat.py.

tuple test_SubsMat.relative_entropy = lo_mat_prot.calculate_relative_entropy(obs_freq_mat)

Definition at line 69 of file test_SubsMat.py.

int test_SubsMat.s = 0

Definition at line 44 of file test_SubsMat.py.