PeptoVar

PeptoVar - Peptides of Variations

Overview

PeptoVar is a program for personalized and population-wide peptidome generation.

• Easy to use (see Usage section).

• Generate peptidomes:

  • personalized for a sample
  • unique peptides for a pair of samples
  • all possible peptides for variations in population

• Translate variations with prefixes and suffixes:

  • determine variation synonymy
  • create translation dependencies

• Has optional parameters for variation filtration and transcript selection.

Requirements

• Linux or MacOS
• python >= 3.5
• pysam module >= 0.11.2.2

Installation

• install pysam package using pip:

  pip3 install pysam

• download latest stable PeptoVar build from this page

• unzip the archive

• add resulting folder to your PATH variable

  • or add symbolic link for PeptoVar script to your bin folder
  • or use PeptoVar directly by specifying full path to the executable script

Usage

Peptides for a sample

This example illustrates usage for sample SAMPLE01:

PeptoVar -samples SAMPLE01 -peptlen 9 -var used -gff ./testdata/test.gff -vcf ./testdata/test.vcf.gz

or

PeptoVar -samples SAMPLE01 -peptlen 9 -var used -indir ./testdata

Unique peptides for a pair of samples

This example illustrates usage for the pair of samples: SAMPLE01 and SAMPLE02:

PeptoVar -samples SAMPLE01 SAMPLE02 -peptlen 9 -var used -gff ./testdata/test.gff -vcf ./testdata/test.vcf.gz

or

PeptoVar -samples SAMPLE01 SAMPLE02 -peptlen 9 -var used -indir ./testdata

Peptides for combinations of variations in the set

This example illustrates usage virtual sample with all variations:

PeptoVar -peptlen 9 -var used -gff ./testdata/test.gff -vcf ./testdata/test.vcf.gz

or

PeptoVar -peptlen 9 -var used -indir ./testdata

Documentation

Detailed PeptoVar description can be found in the manual

If you haven't found the answer to your question in the docs, or have any suggestions concerning new features, feel free to create an issue here, on GitHub, or write an email to dmitry.malko at gmail.com:

License

Copyright (c) 2017, Dmitry Malko All Rights Reserved

PeptoVar is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.