nucleotides_to_matrices package

Submodules

nucleotides_to_matrices.cli module

Console script for nucleotides_to_matrices.

nucleotides_to_matrices.encodings module

Path, data, and lookup dictionaries for IUPAC code vector encodings

nucleotides_to_matrices.encodings.dna_codes()[source]

Set of codes for DNA

nucleotides_to_matrices.encodings.encodings_df()[source]

Data for encodings

nucleotides_to_matrices.encodings.nucleotide_to_vector()[source]

Nucleotide code to vector encoding lookup

nucleotides_to_matrices.encodings.rna_codes()[source]

Set of codes for RNA

nucleotides_to_matrices.encodings.strict_codes()[source]

Set of strict codes

nucleotides_to_matrices.encodings.vector_to_dna()[source]

Vector encoding to DNA code lookup

nucleotides_to_matrices.encodings.vector_to_rna()[source]

Vector encoding to RNA code lookup

nucleotides_to_matrices.nucleotides_to_matrices module

Main module.

nucleotides_to_matrices.nucleotides_to_matrices.matrix_to_sequence(matrix: numpy.ndarray, type: str = 'dna') → str[source]

Convert a matrix of encoded nucleotides into a string.

Parameters:
matrix : numpy.ndarray

Matrix of encoded nucleotides to convert.

type: {‘dna’, ‘rna’}, default ‘dna’

The type of nucleotides to convert to. May be either ‘dna’ or ‘rna’.
Returns:
sequence : string

The converted matrix as a string of nucleotide codes.

See also

sequence_to_matrix
Convert a string of nucleotide codes into a matrix.

Examples

>>> example_dna_sequence = 'GATTACAN'
    >>> dna_matrix = n2m.sequence_to_matrix(example_dna_sequence)
>>> dna_matrix
>>> array([[0, 0, 1, 0],
           [1, 0, 0, 0],
           [0, 0, 0, 1],
           [0, 0, 0, 1],
           [1, 0, 0, 0],
           [0, 1, 0, 0],
           [1, 0, 0, 0],
           [1, 1, 1, 1]])
    >>> dna_sequence = n2m.matrix_to_sequence(dna_matrix)
>>> dna_sequence
'GATTACAN'
>>> example_rna_sequence = 'GAUUACIN'
>>> rna_matrix = n2m.sequence_to_matrix(example_rna_sequence)
>>> rna_matrix
>>> array([[0, 0, 1, 0],
           [1, 0, 0, 0],
           [0, 0, 0, 1],
           [0, 0, 0, 1],
           [1, 0, 0, 0],
           [0, 1, 0, 0],
           [0, 0, 1, 0],
           [1, 1, 1, 1]])
>>> rna_sequence = n2m.matrix_to_sequence(rna_matrix, type = 'rna')
>>> rna_sequence
'GAUUACGN'
nucleotides_to_matrices.nucleotides_to_matrices.sequence_to_matrix(sequence: str) → numpy.ndarray[source]

Convert a string of nucleotide codes into a matrix.

Parameters:
sequence : str

String representing the nucleotides to convert.
Returns:
matrix : numpy.ndarray

The converted string of nucleotide codes as a matrix of integers.

See also

matrix_to_sequence
Converts a matrix into a string of nucleotide codes.

Examples

>>> import nucleotides_to_matrices as n2m
>>> example_dna_sequence = 'GATTACAN'
>>> n2m.sequence_to_matrix(example_dna_sequence)
array([[0, 0, 1, 0],
       [1, 0, 0, 0],
       [0, 0, 0, 1],
       [0, 0, 0, 1],
       [1, 0, 0, 0],
       [0, 1, 0, 0],
       [1, 0, 0, 0],
       [1, 1, 1, 1]])
>>> example_rna_sequence = 'GAUUACIN'
>>> n2m.sequence_to_matrix(example_rna_sequence)
array([[0, 0, 1, 0],
       [1, 0, 0, 0],
       [0, 0, 0, 1],
       [0, 0, 0, 1],
       [1, 0, 0, 0],
       [0, 1, 0, 0],
       [0, 0, 1, 0],
       [1, 1, 1, 1]])

Module contents

Top-level package for Nucleotides To Matrices.

nucleotides_to_matrices.encodings_df()[source]

Data for encodings

nucleotides_to_matrices.sequence_to_matrix(sequence: str) → numpy.ndarray[source]

Convert a string of nucleotide codes into a matrix.

Parameters:
sequence : str

String representing the nucleotides to convert.
Returns:
matrix : numpy.ndarray

The converted string of nucleotide codes as a matrix of integers.

See also

matrix_to_sequence
Converts a matrix into a string of nucleotide codes.

Examples

>>> import nucleotides_to_matrices as n2m
>>> example_dna_sequence = 'GATTACAN'
>>> n2m.sequence_to_matrix(example_dna_sequence)
array([[0, 0, 1, 0],
       [1, 0, 0, 0],
       [0, 0, 0, 1],
       [0, 0, 0, 1],
       [1, 0, 0, 0],
       [0, 1, 0, 0],
       [1, 0, 0, 0],
       [1, 1, 1, 1]])
>>> example_rna_sequence = 'GAUUACIN'
>>> n2m.sequence_to_matrix(example_rna_sequence)
array([[0, 0, 1, 0],
       [1, 0, 0, 0],
       [0, 0, 0, 1],
       [0, 0, 0, 1],
       [1, 0, 0, 0],
       [0, 1, 0, 0],
       [0, 0, 1, 0],
       [1, 1, 1, 1]])
nucleotides_to_matrices.matrix_to_sequence(matrix: numpy.ndarray, type: str = 'dna') → str[source]

Convert a matrix of encoded nucleotides into a string.

Parameters:
matrix : numpy.ndarray

Matrix of encoded nucleotides to convert.

type: {‘dna’, ‘rna’}, default ‘dna’

The type of nucleotides to convert to. May be either ‘dna’ or ‘rna’.
Returns:
sequence : string

The converted matrix as a string of nucleotide codes.

See also

sequence_to_matrix
Convert a string of nucleotide codes into a matrix.

Examples

>>> example_dna_sequence = 'GATTACAN'
    >>> dna_matrix = n2m.sequence_to_matrix(example_dna_sequence)
>>> dna_matrix
>>> array([[0, 0, 1, 0],
           [1, 0, 0, 0],
           [0, 0, 0, 1],
           [0, 0, 0, 1],
           [1, 0, 0, 0],
           [0, 1, 0, 0],
           [1, 0, 0, 0],
           [1, 1, 1, 1]])
    >>> dna_sequence = n2m.matrix_to_sequence(dna_matrix)
>>> dna_sequence
'GATTACAN'
>>> example_rna_sequence = 'GAUUACIN'
>>> rna_matrix = n2m.sequence_to_matrix(example_rna_sequence)
>>> rna_matrix
>>> array([[0, 0, 1, 0],
           [1, 0, 0, 0],
           [0, 0, 0, 1],
           [0, 0, 0, 1],
           [1, 0, 0, 0],
           [0, 1, 0, 0],
           [0, 0, 1, 0],
           [1, 1, 1, 1]])
>>> rna_sequence = n2m.matrix_to_sequence(rna_matrix, type = 'rna')
>>> rna_sequence
'GAUUACGN'