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 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 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 curl/7.72.0
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 /path/to/pseudofinder
- Into the global package database for all users:
$ pip install -U /path/to/pseudofinder
- Into the user package database (for the current user only):
$ pip install -U --user /path/to/pseudofinder
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: