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annotate h-concatenate.R @ 20:8e33abdebc57 draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 14435cfc042911bf1ee409f5a0d5ef908f5feec0-dirty
author tomnl
date Thu, 21 Jun 2018 11:28:11 -0400
parents 55aa2dd24828
children
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55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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1 library(optparse)
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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3 option_list <- list(
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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4 make_option(c("-f", "--files"), type="character"),
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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5 make_option(c("-c", "--columns"), type="character"),
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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6 make_option(c("-o", "--out_dir"), type="character"),
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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7 make_option(c("-u", "--uc"), type="character")
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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8 )
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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10 # store options
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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11 opt<- parse_args(OptionParser(option_list=option_list), args = commandArgs(trailingOnly = TRUE))
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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13 print(sessionInfo())
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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14 print(opt)
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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16 file_paths <- trimws(strsplit(opt$files, ';')[[1]])
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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17 file_paths <- file_paths[file_paths != ""]
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19 columns <- trimws(strsplit(opt$columns, ';')[[1]])
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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20 columns <- columns[columns != ""]
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22 columns <- lapply(columns, function(x){trimws(strsplit(x, ',')[[1]])})
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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25 readIn <- function(f, c){
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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26 print('#### reading in file with columns ####')
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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27 print(f)
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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28 print(c)
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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29 df <- read.table(f, header = TRUE, sep='\t', stringsAsFactors=FALSE)
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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30 if (sum(colnames(df) %in% c)==0){
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31 print('PLEASE CHECK: Selected columns not in file!!')
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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32 print(colnames(df))
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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33 print(c)
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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34 q()
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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35 }
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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37 df <- df[ , (colnames(df) %in% c)]
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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38 if (length(c)==1){
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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39 df <- data.frame(df)
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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40 colnames(df) <- c
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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41 }
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43 return(df)
55aa2dd24828 planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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44 }
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46 m <- mapply(readIn, file_paths, columns, SIMPLIFY = FALSE)
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48 m <- unname(m)
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49 merged <- do.call(cbind, m)
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51 if(!is.null(opt$uc)){
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52 uc <- trimws(strsplit(opt$uc, ',')[[1]])
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53 uc <- uc[uc != ""]
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54 print(colnames(merged))
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55 print(uc)
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56 merged <- merged[uc]
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57 }
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59 print(head(merged))
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61 write.table(merged, file.path(opt$out_dir, 'combined_table.tsv'), row.names=FALSE, sep='\t')
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