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Package Bio :: Package SubsMat |
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Submodules | |
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Classes | |
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SeqMat |
A Generic sequence matrix class The key is a 2-tuple containing the letter indices of the matrix. |
Exceptions | |
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BadMatrix |
Exception raised when verifying a matrix |
Function Summary | |
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make_log_odds_matrix(acc_rep_mat,
exp_freq_table,
logbase,
factor,
round_digit,
keep_nd)
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observed_frequency_to_substitution_matrix(obs_freq_mat)
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read_text_matrix(data_file,
mat_type)
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two_mat_DJS(mat_1,
mat_2,
pi_1,
pi_2)
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two_mat_relative_entropy(mat_1,
mat_2,
logbase,
diag)
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Build an expected frequency matrix exp_freq_table: should be a FreqTable instance | |
_build_log_odds_mat(subs_mat,logbase=10,factor=10.0,round_digit=1): Build a log-odds matrix logbase=2: base of logarithm used to build (default 2) factor=10.: a factor by which each matrix entry is multiplied round_digit: roundoff place after decimal point keep_nd: if true, keeps the -999 value for non-determined values (for which there are no substitutions in the frequency substitutions matrix). | |
build_obs_freq_mat(acc_rep_mat): Build the observed frequency matrix, from an accepted replacements matrix The accRep matrix should be generated by the user. | |
Build the substitution matrix | |
_exp_freq_table_from_obs_freq(obs_freq_mat)
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Variable Summary | |
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int |
ACCREP = 1 |
BadMatrix |
BadMatrixError = <Bio.SubsMat.BadMatrix instance at 0x40...
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int |
diagALL = 3 |
int |
diagNO = 1 |
int |
diagONLY = 2 |
float |
EPSILON = 1e-14 |
int |
EXPFREQ = 4 |
int |
LO = 5 |
int |
NOTYPE = 0 |
int |
OBSFREQ = 2 |
int |
SUBS = 3 |
Function Details |
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_build_exp_freq_mat(exp_freq_table)Build an expected frequency matrix exp_freq_table: should be a FreqTable instance |
_build_log_odds_mat(subs_mat, logbase=2, factor=10.0, round_digit=0, keep_nd=0)_build_log_odds_mat(subs_mat,logbase=10,factor=10.0,round_digit=1): Build a log-odds matrix logbase=2: base of logarithm used to build (default 2) factor=10.: a factor by which each matrix entry is multiplied round_digit: roundoff place after decimal point keep_nd: if true, keeps the -999 value for non-determined values (for which there are no substitutions in the frequency substitutions matrix). If false, plants the minimum log-odds value of the matrix in entries containing -999 |
_build_obs_freq_mat(acc_rep_mat)build_obs_freq_mat(acc_rep_mat): Build the observed frequency matrix, from an accepted replacements matrix The accRep matrix should be generated by the user. |
_build_subs_mat(obs_freq_mat, exp_freq_mat)Build the substitution matrix |
Variable Details |
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ACCREP
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BadMatrixError
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diagALL
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diagNO
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diagONLY
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EPSILON
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EXPFREQ
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LO
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NOTYPE
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OBSFREQ
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SUBS
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