cool_seq_tool.mappers.liftover#

Module for mapping to/from human genome assemblies.

Currently only supports GRCh37 <-> GRCh38

class cool_seq_tool.mappers.liftover.LiftOver(chain_file_37_to_38=None, chain_file_38_to_37=None)[source]#

Class for mapping to/from human genome assemblies

Currently only supports GRCh37 <-> GRCh38

__init__(chain_file_37_to_38=None, chain_file_38_to_37=None)[source]#

Initialize liftover class

Parameters:

  • chain_file_37_to_38 (Optional[str]) – Optional path to chain file for 37 to 38 assembly. This is used for agct. If this is not provided, will check to see if LIFTOVER_CHAIN_37_TO_38 env var is set. If neither is provided, will allow agct to download a chain file from UCSC

  • chain_file_38_to_37 (Optional[str]) – Optional path to chain file for 38 to 37 assembly. This is used for agct. If this is not provided, will check to see if LIFTOVER_CHAIN_38_TO_37 env var is set. If neither is provided, will allow agct to download a chain file from UCSC

get_liftover(chromosome, pos, liftover_to_assembly)[source]#

Get new genome assembly data for a position on a chromosome.

Use a UCSC-style chromosome name:

>>> from cool_seq_tool.mappers import LiftOver
>>> from cool_seq_tool.schemas import Assembly
>>> lo = LiftOver()
>>> lo.get_liftover("chr7", 140453136, Assembly.GRCH38)
('chr7', 140753336)

Chromosome names can also be NCBI-style, without prefixes:

>>> lo.get_liftover("7", 140453136, Assembly.GRCH38)
('chr7', 140753336)
Parameters:

  • chromosome (str) – The chromosome number, e.g. "chr7", "chrX", "5".

  • pos (int) – Position on the chromosome

  • liftover_to_assembly (Assembly) – Assembly to liftover to

Return type:

Optional[tuple[str, int]]

Returns:

Target chromosome and target position for assembly