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VAMPIR.R
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VAMPIR.R
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#!/usr/bin/env Rscript
###########################################################
######################### VAMPIR ##########################
###########################################################
# This script takes multiple input from the software
# ARIBA (github.com/sanger-pathogens/ariba) and
# create summary reports and visualizations. One
# can select specific analyses based on the data you
# have: AMR, virulence, MLST or plasmids.
# Author: Håkon Kaspersen
###########################################################
###########################################################
###########################################################
# ------------------- Libraries --------------------
suppressPackageStartupMessages(library(optparse))
parser <- OptionParser(usage = "Usage: %prog [options] -o output_folder")
# Create command line options
parser <- add_option(parser,
c("-u", "--mut"),
action = "store",
help = "Directory of megaRes reports.")
parser <- add_option(parser,
c("-a", "--acq"),
action = "store",
help = "Directory of resFinder reports.")
parser <- add_option(parser,
c("-i", "--intrinsic"),
action = "store",
help = "List of intrinsic genes of interest, used with -u.
Type 'all' for including all reported genes.
Can partially match gene names, f. ex. 'gyr' will match all gyr genes identified.
Example: -i gyr,par,mar")
parser <- add_option(parser,
c("-q", "--gyrfix"),
action = "store_true",
help = "Add to filter the reported mutations in gyrA, gyrB, parC and parE to those in the QRDR only.")
parser <- add_option(parser,
c("-c", "--acquired"),
action = "store",
help = "List of acquired genes of interest, used with -a.
Type 'all' for including all reported genes.
Can partially match gene names, f. ex. 'qnr' will match all qnr genes identified.
Example: -c blaTEM,oqxAB,qnr")
parser <- add_option(parser,
c("-v", "--vir"),
action = "store",
help = "Directory of ARIBA virulence reports.")
parser <- add_option(parser,
c("-r","--virgenes"),
action = "store",
help = "Virulence genes of interest, use with -v.
Type 'all' for including all reported genes.")
parser <- add_option(parser,
c("-d", "--database"),
action = "store",
help = "Virulence database used: virfinder or vfdb")
parser <- add_option(parser,
c("-m", "--mlst"),
action = "store",
help = "Directory of ARIBA MLST reports.")
parser <- add_option(parser,
c("-p", "--plasmid"),
action = "store",
help = "Directory of ARIBA plasmid reports.")
parser <- add_option(parser,
c("-o", "--output"),
action = "store",
help = "Output directory.
One folder for each analysis will be created
at given location.")
parser <- add_option(parser,
c("-f", "--fileending"),
action = "store",
help = "Ending suffix of result files from ARIBA.")
parser <- add_option(parser,
"--version",
action = "store_true",
help = "Print version info.")
opt <- parse_args(parser)
# Print version info
if (!is.null(opt$version)) {
vi <- R.Version()
print(paste0("VAMPIR ",
system('git describe --tags --abbrev=0',
intern = TRUE),
" run on ",
vi$version.string))
quit()
}
# Check if output folder is specified
if (is.null(opt$output)) {
print("Please specify an output directory.")
quit()
}
## ------------------- Tracks ----------------------
## Intrinsic AMR genes track
if (!is.null(opt$mut)) {
if (is.null(opt$intrinsic)) {
print("Please specify genes of interest with -i.")
stop()
} else if (is.null(opt$fileending)) {
print("Please specify the file endings of input files with -f.")
stop()
} else {
print(paste0(
"Running intrinsic AMR gene summary analysis. Reports location: ",
normalizePath(opt$mut, winslash = "/", mustWork = TRUE),
". Output location: ",
normalizePath(opt$out, winslash = "/", mustWork = TRUE)))
system(paste("Rscript /cluster/projects/nn9305k/vi_src/VAMPIR/src/intrinsic_script.R",
opt$mut,
opt$out,
opt$intrinsic,
opt$fileending,
opt$gyrfix))
}
}
## Acquired AMR genes track
if (!is.null(opt$acq)) {
if (is.null(opt$acquired)) {
print("Please specify genes of interest with -c.")
stop()
} else if (is.null(opt$fileending)) {
print("Please specify the file endings of input files with -f.")
stop()
} else {
print(paste0(
"Running acquired AMR gene summary analysis. Reports location: ",
normalizePath(opt$acq, winslash = "/", mustWork = TRUE),
". Output location: ",
normalizePath(opt$out, winslash = "/", mustWork = TRUE)))
system(paste("Rscript /cluster/projects/nn9305k/vi_src/VAMPIR/src/acquired_script.R",
opt$acq,
opt$out,
opt$acquired,
opt$fileending))
}
}
## Virulence gene track
if (!is.null(opt$vir)) {
if (is.null(opt$database)) {
print("Please specify virulence database used: virfinder, vfdb or vfdb_core.")
stop()
}
if (is.null(opt$virgenes)) {
print("Please specify virulence genes with -r.")
stop()
} else if (is.null(opt$fileending)) {
print("Please specify the file endings of input files with -f.")
stop()
} else {
print(paste0(
"Running virulence gene summary analysis. Reports location: ",
normalizePath(opt$vir, winslash = "/", mustWork = TRUE),
". Output location: ",
normalizePath(opt$out, winslash = "/", mustWork = TRUE),
". Virulence database: ",
opt$database))
system(paste("Rscript /cluster/projects/nn9305k/vi_src/VAMPIR/src/vir_script.R",
opt$vir,
opt$database,
opt$virgenes,
opt$out,
opt$fileending))
}
}
## MLST track
if (!is.null(opt$mlst)) {
if (is.null(opt$fileending)) {
print("Please specify the file endings of input files with -f.")
stop()
} else {
print(paste0(
"Running MLST summary analysis. Reports location: ",
normalizePath(opt$mlst, winslash = "/", mustWork = TRUE),
". Output location: ",
normalizePath(opt$out, winslash = "/", mustWork = TRUE)))
system(paste("Rscript /cluster/projects/nn9305k/vi_src/VAMPIR/src/mlst_script.R",
opt$mlst,
opt$out,
opt$fileending))
}
}
## Plasmid typing track
if (!is.null(opt$plasmid)) {
if (is.null(opt$fileending)) {
print("Please specify the file endings of input files with -f.")
stop()
} else {
print(paste0(
"Running plasmid summary analysis. Reports location: ",
normalizePath(opt$plasmid, winslash = "/", mustWork = TRUE),
". Output location: ",
normalizePath(opt$out, winslash = "/", mustWork = TRUE)))
system(paste("Rscript /cluster/projects/nn9305k/vi_src/VAMPIR/src/plasmid_script.R",
opt$plasmid,
opt$out,
opt$fileending))
}
}