PoolSeqProGen 0.0.2

A package for creating variant protein databases for bacteria from Pool-seq experiments

PoolSeqProGen : a python package for Pool-seq driven proteogenomics protein database creation in bacteria

This python package creates a proteogenomic database from Pooled sequencing experiments by interrogating sorted bam alignment files to include more than one version(due to mutations) of a tryptic peptide. This way it reduces the database size since only those variant sequences containing mutations in a certain order as seen in the alignment file and not all combinations of variant sequences are used. In addition to the tryptic peptides containing mutations, their 'wild type' protein sequences are written to the database. Also the proteins that do not contain mutations are recorded.

Requirements:

It uses pysam,pyteomics and biopython packages.

IF you use this package, please cite:

Weldatsadik RG , Datta N, Kolmeder C, Vuopio J , Kere J , Wilkman SV et al. Pool-seq driven proteogenomic database for Group G Streptococcus . Journal of Proteomics . 2019 June 15; 201: 84-92. https://doi.org/10.1016/j.jprot.2019.04.015

Installation : pip install PoolSeqProGen

usage: generate_variants  [-h] --genbankFile GENBANKFILE
                            --bamFile BAMFILE --SnpEffTextOutputFile
                            SNPEFFTEXTOUTPUTFILE
                            [--geneticCodeID GENETICCODEID]
                            [--fastaFile FASTAFILE] [--poolID POOLID]


optional arguments:
  -h, --help            show this help message and exit

  --genbankFile GENBANKFILE
                        the path to genbank file for the reference genome
  --bamFile BAMFILE     the path to the sorted alignment bam file for
                        retrieving reads from
  --SnpEffTextOutputFile SNPEFFTEXTOUTPUTFILE
                        the path to the text output file from SnpEff. Make sure the
                        chromosome is the same as that found in the bam file.
  --geneticCodeID GENETICCODEID
                        the genetic code id of your species https: //
                        www.ncbi.nlm.nih.gov / Taxonomy / Utils / wprintgc.cgi
  --fastaFile FASTAFILE
                        the path to the fasta output file
  --poolID POOLID       
			Qualifiers to add to the fasta header