Mercurial > repos > tomnl > create_msp
diff anticipated_purity_dims.R @ 0:4b417094bf71 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 0aa10df0ec1ed71601f932cfb11d7d4d4f620d80-dirty
author | tomnl |
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date | Wed, 02 May 2018 13:09:23 -0400 |
parents | |
children | 3f1f2d545f3a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/anticipated_purity_dims.R Wed May 02 13:09:23 2018 -0400 @@ -0,0 +1,138 @@ +library(msPurity) +library(optparse) +print(sessionInfo()) + +option_list <- list( + make_option(c("--mzML_file"), type="character"), + make_option(c("--peaks_file"), type="character"), + make_option(c("-o", "--out_dir"), type="character"), + make_option("--minOffset", default=0.5), + make_option("--maxOffset", default=0.5), + make_option("--ilim", default=0.05), + make_option("--ppm", default=4), + make_option("--dimspy", action="store_true"), + make_option("--sim", action="store_true"), + make_option("--remove_nas", action="store_true"), + make_option("--iwNorm", default="none", type="character"), + make_option("--file_num_dimspy", default=1), + make_option("--exclude_isotopes", action="store_true"), + make_option("--isotope_matrix", type="character") +) + +# store options +opt<- parse_args(OptionParser(option_list=option_list)) + +print(sessionInfo()) +print(opt) + +if (is.null(opt$dimspy)){ + + df <- read.table(opt$peaks_file, header = TRUE, sep='\t') + filename = NA +}else{ + indf <- read.table(opt$peaks_file, + header = TRUE, sep='\t', stringsAsFactors = FALSE) + + filename = colnames(indf)[8:ncol(indf)][opt$file_num_dimspy] + # check if the data file is mzML or RAW (can only use mzML currently) so + # we expect an mzML file of the same name in the same folder + indf$i <- indf[,colnames(indf)==filename] + indf[,colnames(indf)==filename] <- as.numeric(indf[,colnames(indf)==filename]) + + filename = sub("raw", "mzML", filename, ignore.case = TRUE) + + df <- indf[4:nrow(indf),] + if ('blank_flag' %in% colnames(df)){ + df <- df[df$blank_flag==1,] + } + + colnames(df)[colnames(df)=='m.z'] <- 'mz' + + if ('nan' %in% df$mz){ + df[df$mz=='nan',]$mz <- NA + } + df$mz <- as.numeric(df$mz) + + + + +} + +if (!is.null(opt$remove_nas)){ + df <- df[!is.na(df$mz),] +} + +if (is.null(opt$isotope_matrix)){ + im <- NULL +}else{ + im <- read.table(opt$isotope_matrix, + header = TRUE, sep='\t', stringsAsFactors = FALSE) +} + +if (is.null(opt$exclude_isotopes)){ + isotopes <- FALSE +}else{ + isotopes <- TRUE +} + + +if (dir.exists(opt$mzML_file)){ + # if directory then we need to add a file name + print(filename) + if (is.na(filename)){ + print('ERROR: If a directory is provided then a filename needs to be entered + directory or automatically obtained by using a dimspy output') + quit() + }else{ + mzml_file <- file.path(opt$mzML_file, filename) + } +}else{ + mzml_file <- opt$mzML_file +} + +if (is.null(opt$sim)){ + sim=FALSE +}else{ + sim=TRUE +} + +minOffset = as.numeric(opt$minOffset) +maxOffset = as.numeric(opt$maxOffset) + + + +if (opt$iwNorm=='none'){ + iwNorm = FALSE + iwNormFun = NULL +}else if (opt$iwNorm=='gauss'){ + iwNorm = TRUE + iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset) +}else if (opt$iwNorm=='rcosine'){ + iwNorm = TRUE + iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset) +}else if (opt$iwNorm=='QE5'){ + iwNorm = TRUE + iwNormFun = msPurity::iwNormQE.5() +} + +print('FIRST ROWS OF PEAK FILE') +print(head(df)) + +predicted <- msPurity::dimsPredictPuritySingle(df$mz, + filepth=mzml_file, + minOffset=minOffset, + maxOffset=maxOffset, + ppm=opt$ppm, + mzML=TRUE, + sim = sim, + ilim = opt$ilim, + isotopes = isotopes, + im = im, + iwNorm = iwNorm, + iwNormFun = iwNormFun + ) +predicted <- cbind(df, predicted) + +print(head(predicted)) +print(file.path(opt$out_dir, 'anticipated_purity_dims.tsv')) +write.table(predicted, file.path(opt$out_dir, 'anticipated_purity_dims.tsv'), row.names=FALSE, sep='\t')