pyChain

a python pipeline to generate chain files between different genome assemblies for LiftOver.

External Dependencies

This pipeline can only be used under Linux. These softwares must be in your system PATH

• Samtools.
• BLAT or pblat (preferred)
• UCSC tool kits, including:
  • liftUp
  • axtChain
  • chainMergeSort
  • chainSplit
  • chainNet
  • netChainSubset

Installation

Via pip (release only)

pip3 install pyoverchain

Via Github

git clone https://github.com/billzt/pyOverChain.git
cd pyOverChain
python3 setup.py install

Usage

pyoverchain [-h] [-v] [-n NUM_CHROMOSOME_TASKS] [-p NUM_THREADS_PBLAT]
               [--disable-progress]
               old_genome new_genome chr_map

positional arguments:
  old_genome            Old genome file in FASTA format
  new_genome            New genome file in FASTA format
  chr_map               A chromosome-mapping-file in TSV format

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -n NUM_CHROMOSOME_TASKS, --num-chromosome-tasks NUM_CHROMOSOME_TASKS
                        number of parallel tasks to run different chromosomes
                        (default: 2)
  -p NUM_THREADS_PBLAT, --num-threads-pblat NUM_THREADS_PBLAT
                        number of threads for pblat. Only useful if pblat were
                        available (default: 2)
  --disable-progress    Disable progress displaying. Useful if you want to run
                        it in background (default: False)

chromosome-mapping-file

It is a plain text file in TSV format showing the relationship between genome assemblies. Corresponding chromosomes usually have the same or similar names. However, this is not always the case.

#old_genome_chr new_genome_chr
chr1    chr1
chr2    chr2
chr3    chr3

Some useful documents

• Document from kent
• Minimal Steps For LiftOver

Warning

This pipeline can only liftOver different assemblies of the same species.