Package Bio :: Package SubsMat
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Package Bio.SubsMat

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

Classes
SeqMat A Generic sequence matrix class The key is a 2-tuple containing the letter indices of the matrix.

Exceptions
BadMatrix Exception raised when verifying a matrix

Function Summary
  make_log_odds_matrix(acc_rep_mat, exp_freq_table, logbase, factor, round_digit, keep_nd)
  observed_frequency_to_substitution_matrix(obs_freq_mat)
  read_text_matrix(data_file, mat_type)
  two_mat_DJS(mat_1, mat_2, pi_1, pi_2)
  two_mat_relative_entropy(mat_1, mat_2, logbase, diag)
  _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, factor, round_digit, keep_nd)
_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_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
  _exp_freq_table_from_obs_freq(obs_freq_mat)

Variable Summary
int ACCREP = 1                                                                     
BadMatrix BadMatrixError = <Bio.SubsMat.BadMatrix instance at 0x2a...
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

_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

ACCREP

Type:
int
Value:
1                                                                     

BadMatrixError

Type:
BadMatrix
Value:
<Bio.SubsMat.BadMatrix instance at 0x2aaaadfa7320>                     

diagALL

Type:
int
Value:
3                                                                     

diagNO

Type:
int
Value:
1                                                                     

diagONLY

Type:
int
Value:
2                                                                     

EPSILON

Type:
float
Value:
1e-14                                                                 

EXPFREQ

Type:
int
Value:
4                                                                     

LO

Type:
int
Value:
5                                                                     

NOTYPE

Type:
int
Value:
0                                                                     

OBSFREQ

Type:
int
Value:
2                                                                     

SUBS

Type:
int
Value:
3                                                                     

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