Mercurial > repos > iuc > tximport

annotate tximport.R @ 1:2c338211927c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
author iuc
date Thu, 23 Sep 2021 00:18:22 +0000
parents 206a71a69161
children
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206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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1 # setup R error handling to go to stderr
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2 options(show.error.messages = F, error = function() {
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3 cat(geterrmessage(), file = stderr()); q("no", 1, F)
2c338211927c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
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4 })
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206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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9 library("getopt")
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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10 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
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11 args <- commandArgs(trailingOnly = TRUE)
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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13 # get options, using the spec as defined by the enclosed list.
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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14 # we read the options from the default: commandArgs(TRUE).
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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15 spec <- matrix(c(
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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16 "help", "h", 0, "logical",
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17 "out_file", "o", 1, "character",
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18 "countsFiles", "n", 1, "character",
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19 "countsFromAbundance", "r", 1, "character",
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20 "format", "v", 1, "character",
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21 "gff_file", "H", 0, "character",
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22 "tx2gene", "f", 0, "character",
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23 "geneIdCol", "l", 0, "character",
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24 "txIdCol", "p", 1, "character",
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25 "abundanceCol", "i", 0, "character",
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26 "countsCol", "y", 1, "character",
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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27 "lengthCol", "x", 1, "character"),
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28 byrow = TRUE, ncol = 4)
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30 opt <- getopt(spec)
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32 # if help was asked for print a friendly message
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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33 # and exit with a non-zero error code
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34 if (!is.null(opt$help)) {
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35 cat(getopt(spec, usage = TRUE))
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36 q(status = 1)
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37 }
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206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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39 if (is.null(opt$gff_file) & is.null(opt$tx2gene)) {
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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40 cat("A GFF/GTF file or a tx2gene table is required\n")
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41 q(status = 1)
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42 }
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43
1
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44 if (opt$format == "none") { #custom format
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45 if (is.null(opt$txIdCol) | is.null(opt$abundanceCol) | is.null(opt$countsCol) | is.null(opt$lengthCol)) {
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46 cat("If you select a custom format for the input files you need to specify the column names\n")
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47 q(status = 1)
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48 }
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49 }
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51 if (is.null(opt$countsFiles)) {
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52 cat("'countsFiles' is required\n")
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53 q(status = 1)
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54 }
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57 # load samples from tab file
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58 samples_df <- read.table(opt$countsFiles, sep = "\t", header = TRUE)
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59 colnames(samples_df) <- c("id", "path")
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60 rownames(samples_df) <- NULL
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61 # Prepare char vector with files and sample names
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62 files <- file.path(samples_df[, "path"])
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63 names(files) <- samples_df[, "id"]
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67 library(tximport)
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68
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69 ### if the input is a gff/gtf file first need to create the tx2gene table
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70 if (!is.null(opt$gff_file)) {
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71 suppressPackageStartupMessages({
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72 library("GenomicFeatures")
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73 })
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74 txdb <- makeTxDbFromGFF(opt$gff_file)
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75 k <- keys(txdb, keytype = "TXNAME")
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76 tx2gene <- select(txdb, keys = k, columns = "GENEID", keytype = "TXNAME")
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77 # Remove 'transcript:' from transcript IDs (when gffFile is a GFF3 from Ensembl and the transcript does not have a Name)
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78 tx2gene$TXNAME <- sub("^transcript:", "", tx2gene$TXNAME) # nolint
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79
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80 } else {
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81 tx2gene <- read.table(opt$tx2gene, header = FALSE)
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82 }
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86 ##
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87 if (is.null(opt$geneIdCol)) { ## there is a tx2gene table
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88 if (opt$format == "none") { #predefined format
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89 txi_out <- tximport(files, type = "none", txIdCol = opt$txIdCol, abundanceCol = opt$abundanceCol, countsCol = opt$countsCol, lengthCol = opt$lengthCol, tx2gene = tx2gene, countsFromAbundance = opt$countsFromAbundance)
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206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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90 } else {
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91 txi_out <- tximport(files, type = opt$format, tx2gene = tx2gene, countsFromAbundance = opt$countsFromAbundance)
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92 }
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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93 } else { # the gene_ID is a column in the counts table
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94 if (opt$format == "none") { #predefined format
2c338211927c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit b2e8dce6a2cebcc338b0f1b3acefd6ea01fbb418"
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95 txi_out <- tximport(files, type = "none", geneIdCol = opt$geneIdCol, txIdCol = opt$txIdCol, abundanceCol = opt$abundanceCol, countsCol = opt$countsCol, lengthCol = opt$lengthCol, tx2gene = tx2gene, countsFromAbundance = opt$countsFromAbundance)
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206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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96 } else {
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97 txi_out <- tximport(files, type = opt$format, geneIdCol = opt$geneIdCol, countsFromAbundance = opt$countsFromAbundance)
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98 }
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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99
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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100 }
206a71a69161 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
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101 # write count as table
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102 write.table(txi_out$counts, file = opt$out_file, row.names = TRUE, col.names = TRUE, quote = FALSE, sep = "\t")