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comparison plasmidprofile.R @ 1:fc63bfd55903 draft

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author nml
date Fri, 03 Feb 2017 16:34:16 -0500
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0:885bdc903475 1:fc63bfd55903
1 #' RScript capable
2 #' Rscript plasmidprofile.R -b blast_runG.tsv -s srst2_runG.tsv -u 0.75 -l 10000 -t "This is a test" -a
3
4
5 suppressPackageStartupMessages(library("optparse"))
6 suppressPackageStartupMessages(library("Plasmidprofiler"))
7 options(bitmapType='cairo')
8
9 cl_arguments <- function(){
10 # CL arguments ####
11 option_list = list(
12 make_option(c("-b", "--blastfile"), type="character", default=NULL,
13 help="BLAST TSV file name", metavar="character"),
14 make_option(c("-s", "--srst2file"), type="character", default=NULL,
15 help="SRST2 TSV file name", metavar="character"),
16 make_option(c("-u", "--sureness"), type="numeric", default=NA,
17 help="Sureness cut off [default = %default]", metavar="numeric"),
18 make_option(c("-c", "--coverage"), type="numeric", default=NA,
19 help="Percent coverage cut off", metavar="numeric"),
20 make_option(c("-l", "--length"), type="numeric", default=NA,
21 help="Plasmid length cut off", metavar="numeric"),
22 make_option(c("-a", "--anonymize"), action="store_true", default=NA,
23 help="Anonymize plasmid and sample names"),
24 make_option(c("-o", "--outfile"), type="character", default="P2Run_",
25 help="Output filename prefix [default= %default]", metavar="character"),
26 make_option(c("-t", "--title"), type="character", default="Plasmid Profiles",
27 help="Title of image [default = %default]", metavar="character"),
28 make_option(c("-C", "--combineincs"), action="store_true", default=NA,
29 help="Combine very closely related incompatibility groups. eg. ")
30 # make_option(c("-T", "--Test"), action="store_true", default=NA,
31 # help="Test filecache")
32
33 );
34
35 opt_parser <- OptionParser(option_list=option_list);
36 opt <- parse_args(opt_parser);
37
38 if (is.null(opt$blastfile) | is.null(opt$srst2file)){
39 print_help(opt_parser)
40 stop("SRST2 and BLAST files must be supplied.", call.=FALSE)
41 }
42 opt
43 }
44
45
46 opt <- cl_arguments()
47
48 filecache <<- new.env(parent = .GlobalEnv)
49 assign("name", opt$outfile, envir = filecache)
50 assign("mods", "Subsampling applied: ", envir = filecache)
51
52 main(blast.file = opt$blastfile,
53 srst2.file = opt$srst2file,
54 coverage.filter = opt$coverage,
55 sureness.filter = opt$sureness,
56 length.filter = opt$length,
57 anonymize = opt$anonymize,
58 combine.inc = opt$combineincs,
59 main.title = opt$title)