Matrix Module v1.0.0

Data matrix storage and reduction for sequence alignments with unique site pattern compression.

Author:: Mark Kessler
Last Edit:: 3/11/25
Source:: Matrix.py

Exceptions

exception MatrixError(Exception)

This exception is raised when there is an error either in parsing data into the matrix object, or if there is an error during any sort of operation

Matrix

class Matrix

Class that stores and reduces MSA data to only the relevant/unique sites that exist. The only reduction mechanism so far is applicable only to DNA. All other data types will simply be stored in a 2d numpy matrix. Accepts any data that is defined by the Alphabet class in Alphabet.py.

Constructor

__init__(alignment: MSA, alphabet: Alphabet = Alphabet(DNA)) -> None

Takes one single MSA object, along with an Alphabet object, represented as either DNA, RNA, PROTEIN, CODON, or USER. The default is DNA.

Parameter	Type	Description
alignment	MSA	Multiple Sequence Alignment (MSA) object.
alphabet	Alphabet, optional	An alphabet for mapping characters to numerics. Defaults to Alphabet(DNA).

Methods

populate_data -> None

Stores and simplifies the MSA data.

simplify -> None

Reduces the matrix of data by removing non-unique site patterns, and records the location and count of the unique site patterns.

get_ij(i: int, j: int) -> int

Returns the data point at row i, and column j.

Parameter	Type	Description
i	int	row index
j	int	column index

Returns: int: the data point.

get_ij_char(i: int, j: int) -> str

get the character at row i, column j in the character matrix that is associated with the data.

Parameter	Type	Description
i	int	row index
j	int	column index

Returns: str: the character at [i][j]

row_given_name(label: str) -> int

Retrieves the row index of the taxa that has name 'label'

Parameter	Type	Description
label	str	name of a taxon.

Returns: int: a row index

get_seq(label: str) -> np.ndarray

Gets the array of characters for a given taxon.

Parameter	Type	Description
label	str	the name of a taxon.

Returns: np.ndarray: an array of characters, with data type 'U1'.

get_number_seq(label: str) -> np.ndarray

Gets the numerical data for a given taxon with the name 'label'.

Parameter	Type	Description
label	str	name of a taxon

Returns: np.ndarray: a 1 dimensional array of integers, of some specific type

get_column(i: int, data: np.ndarray, sites: int) -> np.ndarray

Returns ith column of a data matrix, with 'sites' elements

Parameter	Type	Description
i	int	column index
data	np.ndarray	a matrix
sites	int	dimension of the column

Returns: np.ndarray: the data at column 'i' with length 'sites'

get_column_at(i: int) -> np.ndarray

Returns ith column of the data matrix

Parameter	Type	Description
i	int	column index

Returns: np.ndarray: the data at column i

site_count -> int

Returns the number of unique sites in the MSA/Data

Returns: int: number of unique sites

populate_counts(new_data: np.ndarray) -> None

Generates a count list that maps the ith distinct column to the number of times it appears in the original alignment matrix.

Parameter	Type	Description
new_data	np.ndarray	The simplified data matrix, that only has distinct column values.

char_matrix -> np.ndarray

Get the character matrix from the matrix of alphabet states.

Returns: np.ndarray: the character matrix, that will have equivalent dimensionality to the state matrix.

get_num_taxa -> int

Get the number of taxa represented in this matrix.

Returns: int: the number of taxa

name_given_row(index: int) -> str

Get the name of the taxa associated with the row of data at 'index'

Parameter	Type	Description
index	int	a row index

Returns: str: the taxon name

get_type -> str

Get the type of data of this matrix

Returns: str: the data type

PhyNetPy Documentation

Matrix Module v1.0.0

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Exceptions

Matrix

Constructor

Methods

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