billzt / pyoverchain

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

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.

pyoverchain's Issues

Working Directory/Mapping File

Hello,
First, thanks for this tool. It's the only one that's been working for me!

However, we've noticed that this tool only runs when both genomes are in the same working directory. Could you clarify this in the documentation?

Error:
mkdir: cannot create directory ‘pyOverChainTmp.NewGenome.axtChain./path/to/genome’: No such file or directory
mkdir: cannot create directory ‘pyOverChainTmp.NewGenome.blat./path/to/genome’: No such file or directory
mkdir: cannot create directory ‘pyOverChainTmp.NewGenome.chain./path/to/genome’: No such file or directory
mkdir: cannot create directory ‘pyOverChainTmp.NewGenome./path/to/genome’: No such file or directory
mkdir: cannot create directory ‘pyOverChainTmp.NewGenome.lift./path/to/genome’: No such file or directory
mkdir: cannot create directory ‘pyOverChainTmp.NewGenome.liftUp./path/to/genome’: No such file or directory
mkdir: cannot create directory ‘pyOverChainTmp.NewGenome.net./path/to/genome’: No such file or directory
mkdir: cannot create directory ‘pyOverChainTmp.NewGenome.over./path/to/genome’: No such file or directory
mkdir: cannot create directory ‘pyOverChainTmp.OldGenome./path/to/genome’: No such file or directory
[pyoverchain:2022-10-26 16:40:12.374990] Begin separating chr1 from /path/to/genome...
sh: pyOverChainTmp.OldGenome./path/to/genome/chr1.fa: No such file or directory
[pyoverchain:2022-10-26 16:40:12.382318] Begin separating chr1 from /path/to/genome...
sh: pyOverChainTmp.NewGenome./path/to/genome/chr1.fa: No such file or directory
[pyoverchain:2022-10-26 16:40:12.390505] Begin separating chr2 from /path/to/genome...
sh: pyOverChainTmp.OldGenome./path/to/genome/chr2.fa: No such file or directory
[pyoverchain:2022-10-26 16:40:12.397635] Begin separating chr2 from /path/to/genome...
sh: pyOverChainTmp.NewGenome./path/to/genome/chr2.fa: No such file or directory

Additionally, I would suggest to integrate creating a mapping file for the two genomes as part of the tool.