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.