Quick start

The Genomic class provides an interface to conversions between genomic positions and coordinates.

>>> from mutalyzer_crossmapper import Genomic
>>> crossmap = Genomic()
>>> crossmap.coordinate_to_genomic(0)
1
>>> crossmap.genomic_to_coordinate(1)
0

On top of the functionality provided by the Genomic class, the NonCoding class provides an interface to conversions between noncoding positions and coordinates.

>>> from mutalyzer_crossmapper import NonCoding
>>> exons = [(5, 8), (14, 20), (30, 35), (40, 44), (50, 52), (70, 72)]
>>> crossmap = NonCoding(exons)
>>> crossmap.coordinate_to_noncoding(35)
(14, 1, 0)
>>> crossmap.noncoding_to_coordinate((14, 1))
35

Add the flag inverted=True to the constructor when the transcript resides on the reverse complement strand.

On top of the functionality provided by the NonCoding class, the Coding class provides an interface to conversions between coding positions and coordinates as well as conversions between protein positions and coordinates.

>>> from mutalyzer_crossmapper import Coding
>>> cds = (32, 43)
>>> crossmap = Coding(exons, cds)
>>> crossmap.coordinate_to_coding(31)
(-1, 0, -1, 0)
>>> crossmap.coding_to_coordinate((-1, 0, -1))
31

Again, the flag inverted=True can be used for transcripts that reside on the reverse complement strand.

Conversions between protein positions and coordinates are done as follows.

>>> crossmap.coordinate_to_protein(41)
(2, 2, 0, 0, 0)
>>> crossmap.protein_to_coordinate((2, 2, 0, 0))
41