| Previous changeset 0:885bdc903475 (2017-02-03) Next changeset 2:842d76e75fbe (2017-03-03) |
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plasmidprofile.R |
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| diff -r 885bdc903475 -r fc63bfd55903 plasmidprofile.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plasmidprofile.R Fri Feb 03 16:34:16 2017 -0500 |
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| @@ -0,0 +1,59 @@ +#' RScript capable +#' Rscript plasmidprofile.R -b blast_runG.tsv -s srst2_runG.tsv -u 0.75 -l 10000 -t "This is a test" -a + + +suppressPackageStartupMessages(library("optparse")) +suppressPackageStartupMessages(library("Plasmidprofiler")) +options(bitmapType='cairo') + +cl_arguments <- function(){ + # CL arguments #### + option_list = list( + make_option(c("-b", "--blastfile"), type="character", default=NULL, + help="BLAST TSV file name", metavar="character"), + make_option(c("-s", "--srst2file"), type="character", default=NULL, + help="SRST2 TSV file name", metavar="character"), + make_option(c("-u", "--sureness"), type="numeric", default=NA, + help="Sureness cut off [default = %default]", metavar="numeric"), + make_option(c("-c", "--coverage"), type="numeric", default=NA, + help="Percent coverage cut off", metavar="numeric"), + make_option(c("-l", "--length"), type="numeric", default=NA, + help="Plasmid length cut off", metavar="numeric"), + make_option(c("-a", "--anonymize"), action="store_true", default=NA, + help="Anonymize plasmid and sample names"), + make_option(c("-o", "--outfile"), type="character", default="P2Run_", + help="Output filename prefix [default= %default]", metavar="character"), + make_option(c("-t", "--title"), type="character", default="Plasmid Profiles", + help="Title of image [default = %default]", metavar="character"), + make_option(c("-C", "--combineincs"), action="store_true", default=NA, + help="Combine very closely related incompatibility groups. eg. ") + # make_option(c("-T", "--Test"), action="store_true", default=NA, + # help="Test filecache") + + ); + + opt_parser <- OptionParser(option_list=option_list); + opt <- parse_args(opt_parser); + + if (is.null(opt$blastfile) | is.null(opt$srst2file)){ + print_help(opt_parser) + stop("SRST2 and BLAST files must be supplied.", call.=FALSE) + } + opt +} + + +opt <- cl_arguments() + +filecache <<- new.env(parent = .GlobalEnv) +assign("name", opt$outfile, envir = filecache) +assign("mods", "Subsampling applied: ", envir = filecache) + +main(blast.file = opt$blastfile, + srst2.file = opt$srst2file, + coverage.filter = opt$coverage, + sureness.filter = opt$sureness, + length.filter = opt$length, + anonymize = opt$anonymize, + combine.inc = opt$combineincs, + main.title = opt$title) |