This program tries to find processed pseudo genes in genome sequencing data using input structural variant calls and the coordinates of gene exons.
In the examples below, $
indicates the command line prompt.
This is a test branch.
This program is released as open source software under the terms of MIT License.
You can install pseudofinder directly from the source code.
Clone this repository:
git clone -b multiexons --single-branch https://github.com/bjpop/pseudofinder
The program depends on cyvcf2, which depends on htslib, which depends on curl. To install you may need the curl library available. On Spartan this can be achieved with:
module load gcccore/8.3.0
module load curl/7.72.0
module load python/3.8.2
Move into the repository directory:
cd pseudofinder
Python 3 is required for this software.
Psuedofinder can be installed using pip
in a variety of ways ($
indicates the command line prompt):
- Inside a virtual environment:
python3 -m venv pseudofinder_dev
source pseudofinder_dev/bin/activate
pip install -U $(pwd)
- Into the global package database for all users:
pip install -U $(pwd)
- Into the user package database (for the current user only):
pip install -U --user $(pwd)
pseudofinder --exons hg19.genes.exons.txt --log example.log --sample sample_name sv_vcf_file.vcf > sample_name.psuedo.csv
Psuedofinder can display usage information on the command line via the -h
or --help
argument:
$ pseudofinder -h
usage: pseudofinder [-h] --exons FILEPATH --sample STR [--version] [--log LOG_FILE] FILEPATH
Read one or more FASTA files, compute simple stats for each file
positional arguments:
FILEPATH Filepaths of VCF file containing structural variant calls
optional arguments:
-h, --help show this help message and exit
--exons FILEPATH Filepath of file containing exon coordinates for genes of interest
--sample STR Name of sample
--version show program's version number and exit
--log LOG_FILE record program progress in LOG_FILE
Psuedofinder returns the following exit status values:
- 0: The program completed successfully.
- 1: File I/O error
- 2: Command line error
- 3: VCF file error
Please submit bug reports and feature requests to the issue tracker on GitHub: