Crossmapper

class mutalyzer_crossmapper.crossmapper.Genomic

Genomic crossmap object.

coordinate_to_genomic(coordinate)

Convert a coordinate to a genomic position (g./m./o.).

Parameters

coordinate (int) – Coordinate.

Returns int

Genomic position.

genomic_to_coordinate(position)

Convert a genomic position (g./m./o.) to a coordinate.

Parameters

position (int) – Genomic position.

Returns int

Coordinate.

class mutalyzer_crossmapper.crossmapper.NonCoding(locations, inverted=False)

NonCoding crossmap object.

Parameters
  • locations (list) – List of locus locations.

  • inverted (bool) – Orientation.

coordinate_to_genomic(coordinate)

Convert a coordinate to a genomic position (g./m./o.).

Parameters

coordinate (int) – Coordinate.

Returns int

Genomic position.

coordinate_to_noncoding(coordinate)

Convert a coordinate to a noncoding position (n./r.).

Parameters

coordinate (int) – Coordinate.

Returns tuple

Noncoding position.

genomic_to_coordinate(position)

Convert a genomic position (g./m./o.) to a coordinate.

Parameters

position (int) – Genomic position.

Returns int

Coordinate.

noncoding_to_coordinate(position)

Convert a noncoding position (n./r.) to a coordinate.

Parameters

position (tuple) – Noncoding position.

Returns int

Coordinate.

class mutalyzer_crossmapper.crossmapper.Coding(locations, cds, inverted=False)

Coding crossmap object.

Parameters
  • locations (list) – List of locus locations.

  • cds (tuple) – Locus location.

  • inverted (bool) – Orientation.

coding_to_coordinate(position)

Convert a coding position (c./r.) to a coordinate.

Parameters

position (tuple) – Coding position (c./r.).

Returns int

Coordinate.

coordinate_to_coding(coordinate, degenerate=False)

Convert a coordinate to a coding position (c./r.).

Parameters
  • coordinate (int) – Coordinate.

  • degenerate (bool) – Return a degenerate position.

Returns tuple

Coding position (c./r.).

coordinate_to_genomic(coordinate)

Convert a coordinate to a genomic position (g./m./o.).

Parameters

coordinate (int) – Coordinate.

Returns int

Genomic position.

coordinate_to_noncoding(coordinate)

Convert a coordinate to a noncoding position (n./r.).

Parameters

coordinate (int) – Coordinate.

Returns tuple

Noncoding position.

coordinate_to_protein(coordinate)

Convert a coordinate to a protein position (p.).

Parameters

coordinate (int) – Coordinate.

Returns tuple

Protein position (p.).

genomic_to_coordinate(position)

Convert a genomic position (g./m./o.) to a coordinate.

Parameters

position (int) – Genomic position.

Returns int

Coordinate.

noncoding_to_coordinate(position)

Convert a noncoding position (n./r.) to a coordinate.

Parameters

position (tuple) – Noncoding position.

Returns int

Coordinate.

protein_to_coordinate(position)

Convert a protein position (p.) to a coordinate.

Parameters

position (tuple) – Protein position (p.).

Returns int

Coordinate.