Overview

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.

Licence

This program is released as open source software under the terms of MIT License.

Installing

You can install pseudofinder directly from the source code.

Installing directly from 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):

1. Inside a virtual environment:

$ python3 -m venv pseudofinder_dev
$ source pseudofinder_dev/bin/activate
$ pip install -U /path/to/pseudofinder

2. Into the global package database for all users:

$ pip install -U /path/to/pseudofinder

3. Into the user package database (for the current user only):

$ pip install -U --user /path/to/pseudofinder

General behaviour

Example

pseudofinder --exons hg19.genes.exons.txt --log example.log --sample sample_name sv_vcf_file.vcf > sample_name.psuedo.csv 

Help message

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

Exit status values

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

Bug reporting and feature requests

Please submit bug reports and feature requests to the issue tracker on GitHub:

pseudofinder issue tracker