--- a/create_msp.R	Wed Jul 18 06:04:14 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,200 +0,0 @@
-suppressWarnings(suppressPackageStartupMessages(require(optparse,quietly = T)))
-suppressWarnings(suppressPackageStartupMessages(require(msPurity)))
-print(sessionInfo())
-# Get the parameter
-option_list <- list(
-  make_option(c("-i","--purity"),type="character"),
-  make_option(c("-p","--ppm"),type="numeric"),
-  make_option(c("-m","--mode"),type="character")
-)
-opt <- parse_args(OptionParser(option_list=option_list))
-
-print(opt)
-
-load(opt$purity)
-
-grped_df <- pa@grped_df
-
-msms <- pa@grped_ms2
-
-puritydf <- pa@puritydf
-
-
-
-#grped_df$fileid <- sapply(grped_df$filename, function(x) which(basename(pa@fileList)==x))
-#puritydf$fileid <- sapply(puritydf$filename, function(x) which(basename(pa@fileList)==x))
-
-
-
-
-selfrag <- as.numeric(unique(grped_df$grpid)) 
-
-of <- file(description = "outfile.msp", open = "w+a")
-
-write.msp <- function(name,precmz,prectype,spectra,ofile){
-
-    cat(paste("NAME: ", name, "\r\n", sep = ""), file = ofile)
-
-    cat(paste("PRECURSORMZ: ", precmz , "\r\n", sep = ""), file = ofile)
-
-    #cat(paste("PRECURSORTYPE: ", prectype, "\r\n", sep = ""), file = ofile) # No adducts? Annotation
-
-    cat("Comment:\r\n", file = ofile)
-
-    cat(paste("Num Peaks: ", nrow(spectra), "\r\n", sep = ""), file = ofile)
-
-    cat(paste(paste(spectra[,1], spectra[,2], sep = "\t"), sep = "\r\n"), sep = "\r\n", file = ofile)
-
-    cat("\r\n", file = ofile)
-}
-
-for(i in selfrag){
-
-    j <- which(grped_df$grpid==i) 
-
-    spec <- msms[[as.character(i)]]
-
-    if (length(j)>1){
-
-        grpd <- grped_df[j,] 
-
-        if (opt$mode=="all"){ 
-
-            for(jj in 1:length(j)){
-
-                idj <- paste(i,jj,sep=".")
-
-                specj <- spec[[jj]]
-
-
-
-                grpdj <- grpd[jj,]
-                if ('sample' %in% colnames(grpd)){
-                    fileid = grpdj$sample
-                }else{
-                    fileid = grpdj$fileid
-                }
-                name = paste(i, fileid, grpdj$pid, sep='-')
-
-                write.msp(name,grpdj$precurMtchMZ,"",specj,of)
-            }
-
-        }else{
-
-            prec_int <- sapply(grpd$precurMtchID, function(x) puritydf[ which(puritydf$seqNum==x & puritydf$fileid==grpd$fileid[1]), "precursorIntensity"] )
-
-            if (opt$mode=="max"){
-
-                idx <- which(prec_int==max(prec_int))
-
-                grpd <- grpd[idx,]
-                if ('sample' %in% colnames(grpd)){
-                    fileid = grpd$sample
-                }else{
-                    fileid = grpd$fileid
-                }
-
-                name = paste(i, fileid, grpd$pid, sep='-')
-                write.msp(name,grpd$precurMtchMZ,"",specj[[idx]], of)
-            }
-
-            if (opt$mode=="average"){
-
-                file_weights <- prec_int/prec_int[which(prec_int==min(prec_int))] # spectra of the most intense precursor, largest weight
-
-                merged_msms <- do.call("rbind", spec)
-
-                colnames(merged_msms) <- c("mz","int")
-
-                file_weights <-rep(file_weights,sapply(spec,nrow))
-
-                merged_msms <- data.frame(cbind(merged_msms,file_weights))
-
-                umzs <- sort(merged_msms$mz,index.return=T)$ix
-
-                merged_msms <- merged_msms[umzs,]
-
-                umzs <- merged_msms$mz
-
-                mz_groups <- list() # mz windows to bind
-
-                mz_grouped <- c() # used mzs
-
-                ppm <- opt$ppm # ppm level to bind mzs
-
-                for(y in 1:length(umzs)){ # spectra averaging
-                    
-                    z <- umzs[y]
-                    
-                    if(!(z %in% mz_grouped)){
-
-                        mz_range <- z*(ppm/1e6)
-
-                        mz_range <- c(z-mz_range,z+mz_range)
-
-                        mz_group <- which(umzs>mz_range[1] & umzs<mz_range[2])
-
-                        if(length(mz_group)>1){
-
-                            zz <- umzs[max(mz_group)]
-                    
-                            mz_range <- zz*(ppm/1e6)
-                    
-                                mz_range <- c(zz-mz_range,zz+mz_range)
-
-                                mz_group2 <- which(umzs>mz_range[1] & umzs<mz_range[2])
-
-                                mz_group <- append(mz_group,mz_group2)
-                        }
-
-                        mz_group <- unique(mz_group)
-
-                        mz_grouped <- append(mz_grouped,umzs[mz_group])
-
-                        mz_group <- list(mz_group)
-
-                        mz_groups <- append(mz_groups,mz_group)
-                        }
-                    }
-
-                    averaged_spec <- t(sapply(mz_groups,function(x){
-                    
-                    if(length(x)==1){
-
-                        mz <- merged_msms$mz[x]
-
-                        nint <- merged_msms[x,]
-
-                        nint <- nint$int*nint$file_weights
-
-                    }else{
-
-                        mz <- mean(merged_msms$mz[x])
-                    
-                        nint <- sum(sapply(x,function(y){
-                          nint <- merged_msms[y,]
-                          nint <- nint$int*nint$file_weights
-                        }))
-                    }
-                        return(c(mz,nint))
-                    }))
-                    
-                    write.msp(i,mean(grpd$precurMtchMZ),"",averaged_spec,of)
-
-            }
-        }
-    }else{
-        spec <- spec[[1]]
-
-        grpd <- grped_df[j,]
-        if ('sample' %in% colnames(grpd)){
-            fileid = grpd$sample
-        }else{
-            fileid = grpd$fileid
-        }
-        name = paste(i, fileid, grpd$pid, sep='-')
-        write.msp(name,grpd$precurMtchMZ,"",spec,of)
-    }
-}
-
-