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Step by Step Guide
CPgeneProfiler uses NCBI BLAST+ installed in Unix/Linux system and R framework to profile CP genes from genome assemblies. Currently, CPgeneProfiler database includes the following CP gene families: IMI, IMP, KPC, NDM, OXA, VIM
Step 1A: Linux package installation (Reference: Standalone BLAST Setup for Unix)
Go to page: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/
Save ncbi-blast-2.9.0+-x64-linux.tar.gz in the local directory
To install, simply extract the downloaded package after placing it under a desired directory. This can be accomplished by a single tar command, or a combination of gunzip and tar commands in Unix/Linux terminal.
$ tar zxvpf ncbi-blast-2.9.0+-x64-linux.tar.gz
Under bash, the following command appends the path to the new BLAST bin directory to the existing PATH setting:
$ export PATH=$PATH:$HOME/ncbi-blast-2.9.0+/bin
To install multiple packages used by CPgeneProfiler, in the Rstudio console run the following command:
install.packages(c("ggplot2","dplyr", "tidyverse", "UpSetR", "scales", "ape", "reshape2", "gridExtra"))
> source("https://bioconductor.org/biocLite.R")
> biocLite("Biostrings")
> install.packages("BiocManager")
> BiocManager::install(c("Biostrings"))
Install devtools first, and then need to load them:
> install.packages(devtools)
> library(devtools)
Then install the CPgeneProfiler package using devtools. While installing, switching off to upgrade dependencies
devtools::install_github("ramadatta/CPgeneProfiler")
Ensure you have installed the package properly by running following command in R console:
?CPgeneProfiler
> url <- "https://raw.githubusercontent.com/ramadatta/CPgene-profiler/master/ARG-annot_CPGene_DB.fasta"
> path <- "/home/user/db" # Can change to preferable location
> setwd(path)
> destfile <- "ARG-annot_CPGene_DB.fasta"
> download.file(url, destfile)
Step 7: Run the CPgeneProfiler package in console providing fasta file folder location and ARG-annot database location
> CPgeneProfiler("/home/user/testData/fasta","/home/user/testData/db/")