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):

1. Inside a virtual environment:

python3 -m venv pseudofinder_dev
source pseudofinder_dev/bin/activate
pip install -U $(pwd)

2. Into the global package database for all users:

pip install -U $(pwd)

3. 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:

pseudofinder issue tracker