Mercurial > repos > melpetera > generic_filter

comparison GalFilter/filter_wrap.R @ 3:cfd7c4aa5c26 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author melpetera
date Fri, 03 Jan 2020 04:09:28 -0500
parents 2c9afaf849ad
children
comparison
equal deleted inserted replaced
2:12cf1eed21f4 3:cfd7c4aa5c26
8 # Original data: used with filter_script.R # 8 # Original data: used with filter_script.R #
9 # Starting date: 04-09-2014 # 9 # Starting date: 04-09-2014 #
10 # V-1: Restriction of old filter wrapper to Filter according to factors # 10 # V-1: Restriction of old filter wrapper to Filter according to factors #
11 # V-1.1: Modification to allow the choice of meta-data table for filtering # 11 # V-1.1: Modification to allow the choice of meta-data table for filtering #
12 # V-2: Addition of numerical filter # 12 # V-2: Addition of numerical filter #
13 # V-2.5: -h option + additional information in stdout #
13 # # 14 # #
14 # # 15 # #
15 # Input files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt # 16 # Input files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt #
16 # Output files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt # 17 # Output files: dataMatrix.txt ; sampleMetadata.txt ; variableMetadata.txt #
17 # # 18 # #
18 ################################################################################################ 19 ################################################################################################
19 20
20 21
21 library(batch) #necessary for parseCommandArgs function 22 library(batch) #necessary for parseCommandArgs function
23
24 # Constants
25 argv <- commandArgs(trailingOnly = FALSE)
26 script.path <- sub("--file=","",argv[grep("--file=",argv)])
27 prog.name <- basename(script.path)
28
29 # Help
30 if (length(grep('-h', argv)) >0) {
31 cat("Usage:", prog.name,
32 "dataMatrix_in myDataMatrix.tsv",
33 "sampleMetadata_in mySampleMetadata.tsv",
34 "variableMetadata_in myVariableMetadata.tsv",
35 "...",
36 "\n")
37 quit(status = 0)
38 }
39
22 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects 40 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
23 41
24 source_local <- function(...){ 42 source_local <- function(...){
25 argv <- commandArgs(trailingOnly = FALSE) 43 argv <- commandArgs(trailingOnly = FALSE)
26 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) 44 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
29 #Import the different functions 47 #Import the different functions
30 source_local("filter_script.R","RcheckLibrary.R","miniTools.R") 48 source_local("filter_script.R","RcheckLibrary.R","miniTools.R")
31 49
32 50
33 if(length(args) < 8){ stop("NOT enough argument !!!") } 51 if(length(args) < 8){ stop("NOT enough argument !!!") }
52
53
54 cat('\nJob starting time:\n',format(Sys.time(), "%a %d %b %Y %X"),
55 '\n\n--------------------------------------------------------------------',
56 '\nParameters used in "Generic Filter":\n\n')
57 print(args)
58 cat('--------------------------------------------------------------------\n\n')
59
34 60
35 list_num <- NULL 61 list_num <- NULL
36 if(!is.null(args$parm_col)){ 62 if(!is.null(args$parm_col)){
37 for( i in which(names(args)=="num_file") ){ 63 for( i in which(names(args)=="num_file") ){
38 if(args[[i+2]] %in% c("lower","upper")){ 64 if(args[[i+2]] %in% c("lower","upper")){
57 83
58 #filters(ion.file.in, meta.samp.file.in, meta.ion.file.in, 84 #filters(ion.file.in, meta.samp.file.in, meta.ion.file.in,
59 # NUM, ls.num, FACT, ls.fact, 85 # NUM, ls.num, FACT, ls.fact,
60 # ion.file.out, meta.samp.file.out, meta.ion.file.out) 86 # ion.file.out, meta.samp.file.out, meta.ion.file.out)
61 87
88
89 cat('\n--------------------------------------------------------------------',
90 '\nInformation about R (version, Operating System, attached or loaded packages):\n\n')
91 sessionInfo()
92 cat('--------------------------------------------------------------------\n',
93 '\nJob ending time:\n',format(Sys.time(), "%a %d %b %Y %X"))
94
95
62 #delete the parameters to avoid the passage to the next tool in .RData image 96 #delete the parameters to avoid the passage to the next tool in .RData image
63 rm(args) 97 rm(args)