README for gammaBOriS and gammaBOriTax

as described in Sperlea et al., "gammaBOriS: Identification and Taxonomic Classification of Origins of Replication in Gammaproteobacteria using Motif-based Machine Learning", Sci Rep (2020). 

-- Intro:

This package contains gammaBOriS, a tool written in R that identifies origin of replication (oriC) sequences in gammaproteobacterial chromosomes, and gammaBOriTax, a bash script that classifies oriC sequences as identified by gammaBOriS taxonomically.

-- Usage:

gammaBOris:

Rscript [location of gammaBOriS.R/]gammaBOriS.R [arguments]

Arguments, separated by single spaces, all mandatory:
1. Input file (with path) containing a DNA sequences in fasta format
2. Path to folder where the output of gammaBOriS will be written to
3. Path to folder that contains the seed and model file included in this package and gkmpredict, which can be obtained at https://github.com/Dongwon-Lee/lsgkm

Requirements: Aside from gkmpredict and all its requirements, the packages BioStrings and stringr need to be installed




gammaBOriTax:

gammaBOriTax.sh [arguments]

Arguments, separated by single spaces, all mandatory:
1. Input file (with) containing a single, 1250 bp long DNA sequence in fasta format
2. Folder for temp files, empty
3. Path of the folder the model files included in the subfolder models/ in this package are stored 
4. Path to folder where the output of gammaBOriTax will be written to
4. Path of gkmpredict, which can be obtained at https://github.com/Dongwon-Lee/lsgkm

Requirements: gkmpredict and all its requirements
