Bio.SubsMat

Package Bio :: Package SubsMat

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Package Bio.SubsMat

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

Submodules
`FreqTable` `MatrixInfo`: A whole bunch of substitution matrices for use in alignments, etc.

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)`

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

Variable Details

ACCREP

Type:: int
Value:: 1

BadMatrixError

Type:: BadMatrix
Value:: <Bio.SubsMat.BadMatrix instance at 0x2aaaabbbe3b0>

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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