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431dec3764
* Added SubsMat tests, sample files and expected outputs. * Updated alignment test to use SubsMat.FreqTable.
41 lines
1.5 KiB
Python
41 lines
1.5 KiB
Python
import cPickle
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import sys
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from Bio.SubsMat import *
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f = sys.stdout
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ftab_prot = FreqTable.read_count(open('SubsMat/protein_count.txt'))
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ctab_prot = FreqTable.read_freq(open('SubsMat/protein_freq.txt'))
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f.write("Check differences between derived and true frequencies for each\n")
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f.write("letter. Differences should be very small\n")
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for i in ftab_prot.alphabet.letters:
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f.write("%s %f\n" % (i, abs(ftab_prot[i] - ctab_prot[i])))
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acc_rep_mat = cPickle.load(open('SubsMat/acc_rep_mat.pik'))
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acc_rep_mat = SubsMat.SeqMat(acc_rep_mat)
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obs_freq_mat = SubsMat._build_obs_freq_mat(acc_rep_mat)
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ftab_prot2 = SubsMat._exp_freq_table_from_obs_freq(obs_freq_mat)
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obs_freq_mat.print_mat(f=f,format=" %4.3f")
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f.write("Diff between supplied and matrix-derived frequencies, should be small\n")
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for i in ftab_prot.keys():
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f.write("%s %.2f\n" % (i,abs(ftab_prot[i] - ftab_prot2[i])))
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s = 0.
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f.write("Calculating sum of letters for an observed frequency matrix\n")
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obs_freq_mat.all_letters_sum()
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for i in obs_freq_mat.sum_letters.keys():
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f.write("%s\t%.2f\n" % (i, obs_freq_mat.sum_letters[i]))
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s += obs_freq_mat.sum_letters[i]
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f.write("Total sum %.2f should be 1.0\n" % (s))
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lo_mat_prot = \
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SubsMat.make_log_odds_matrix(acc_rep_mat=acc_rep_mat,round_digit=1) #,ftab_prot
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f.write("\nLog odds matrix\n")
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lo_mat_prot.print_mat(f=f,format=" %.2f",alphabet='AVILMCFWYHSTNQKRDEGP')
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f.write("\nTesting MatrixInfo\n")
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for i in MatrixInfo.available_matrices:
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mat = SubsMat.SeqMat(getattr(MatrixInfo,i))
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f.write("\n%s\n------------\n" % i)
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mat.print_mat(f=f)
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