Package Bio :: Package SubsMat
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Package SubsMat

source code

Substitution matrices, log odds matrices, and operations on them.

Submodules [hide private]

Classes [hide private]
  BadMatrix
Exception raised when verifying a matrix
  SeqMat
A Generic sequence matrix class The key is a 2-tuple containing the letter indices of the matrix.
Functions [hide private]
 
_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.
source code
 
_exp_freq_table_from_obs_freq(obs_freq_mat) source code
 
_build_exp_freq_mat(exp_freq_table)
Build an expected frequency matrix exp_freq_table: should be a FreqTable instance
source code
 
_build_subs_mat(obs_freq_mat, exp_freq_mat)
Build the substitution matrix
source code
 
_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).
source code
 
make_log_odds_matrix(acc_rep_mat, exp_freq_table=None, logbase=2, factor=1.0, round_digit=9, keep_nd=0) source code
 
observed_frequency_to_substitution_matrix(obs_freq_mat) source code
 
read_text_matrix(data_file, mat_type=0) source code
 
two_mat_relative_entropy(mat_1, mat_2, logbase=2, diag=3) source code
 
two_mat_DJS(mat_1, mat_2, pi_1=0.5, pi_2=0.5) source code
Variables [hide private]
  NOTYPE = 0
  ACCREP = 1
  OBSFREQ = 2
  SUBS = 3
  EXPFREQ = 4
  LO = 5
  EPSILON = 1e-14
  BadMatrixError = BadMatrix()
  diagNO = 1
  diagONLY = 2
  diagALL = 3
  __package__ = 'Bio.SubsMat'
Function Details [hide private]

_build_log_odds_mat(subs_mat, logbase=2, factor=10.0, round_digit=0, keep_nd=0)

source code 

_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