Mercurial > repos > iuc > tximport
comparison tximport.R @ 0:206a71a69161 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tximport commit 66c3b86403faa115751332ea8e0383e26b9ee599"
author | iuc |
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date | Wed, 04 Dec 2019 05:57:26 -0500 |
parents | |
children | 2c338211927c |
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-1:000000000000 | 0:206a71a69161 |
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1 # setup R error handling to go to stderr | |
2 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | |
3 | |
4 # we need that to not crash galaxy with an UTF8 error on German LC settings. | |
5 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | |
6 | |
7 library("getopt") | |
8 options(stringAsFactors = FALSE, useFancyQuotes = FALSE) | |
9 args <- commandArgs(trailingOnly = TRUE) | |
10 | |
11 # get options, using the spec as defined by the enclosed list. | |
12 # we read the options from the default: commandArgs(TRUE). | |
13 spec <- matrix(c( | |
14 "help", "h", 0, "logical", | |
15 "out_file", "o", 1, "character", | |
16 "countsFiles", "n", 1, "character", | |
17 "countsFromAbundance", "r", 1, "character", | |
18 "format", "v", 1, "character", | |
19 "gff_file", "H", 0, "character", | |
20 "tx2gene", "f", 0, "character", | |
21 "geneIdCol", "l", 0, "character", | |
22 "txIdCol" , "p", 1, "character", | |
23 "abundanceCol", "i", 0, "character", | |
24 "countsCol", "y", 1, "character", | |
25 "lengthCol", "x", 1, "character"), | |
26 byrow=TRUE, ncol=4) | |
27 | |
28 opt <- getopt(spec) | |
29 | |
30 # if help was asked for print a friendly message | |
31 # and exit with a non-zero error code | |
32 if (!is.null(opt$help)) { | |
33 cat(getopt(spec, usage=TRUE)) | |
34 q(status=1) | |
35 } | |
36 | |
37 if (is.null(opt$gff_file) & is.null(opt$tx2gene)) { | |
38 cat("A GFF/GTF file or a tx2gene table is required\n") | |
39 q(status=1) | |
40 } | |
41 | |
42 if (opt$format == 'none'){ #custom format | |
43 if (is.null(opt$txIdCol) | is.null(opt$abundanceCol) | is.null(opt$countsCol) | is.null(opt$lengthCol)) { | |
44 cat("If you select a custom format for the input files you need to specify the column names\n") | |
45 q(status=1) | |
46 } | |
47 } | |
48 | |
49 if (is.null(opt$countsFiles)) { | |
50 cat("'countsFiles' is required\n") | |
51 q(status=1) | |
52 } | |
53 | |
54 | |
55 # load samples from tab file | |
56 samples_df <- read.table(opt$countsFiles, sep="\t", header=TRUE) | |
57 colnames(samples_df) <- c("id","path") | |
58 rownames(samples_df) <- NULL | |
59 # Prepare char vector with files and sample names | |
60 files <- file.path(samples_df[,"path"]) | |
61 names(files) <- samples_df[,"id"] | |
62 | |
63 | |
64 | |
65 library(tximport) | |
66 | |
67 ### if the input is a gff/gtf file first need to create the tx2gene table | |
68 if (!is.null(opt$gff_file)) { | |
69 suppressPackageStartupMessages({ | |
70 library("GenomicFeatures") | |
71 }) | |
72 txdb <- makeTxDbFromGFF(opt$gff_file) | |
73 k <- keys(txdb, keytype = "TXNAME") | |
74 tx2gene <- select(txdb, keys=k, columns="GENEID", keytype="TXNAME") | |
75 # Remove 'transcript:' from transcript IDs (when gffFile is a GFF3 from Ensembl and the transcript does not have a Name) | |
76 tx2gene$TXNAME <- sub('^transcript:', '', tx2gene$TXNAME) | |
77 | |
78 } else { | |
79 tx2gene <- read.table(opt$tx2gene,header=FALSE) | |
80 } | |
81 | |
82 | |
83 | |
84 ## | |
85 if (is.null(opt$geneIdCol)) { ## there is a tx2gene table | |
86 if (opt$format == 'none'){ #predefined format | |
87 txi_out <- tximport(files, type="none",txIdCol=opt$txIdCol,abundanceCol=opt$abundanceCol,countsCol=opt$countsCol,lengthCol=opt$lengthCol,tx2gene=tx2gene,countsFromAbundance=opt$countsFromAbundance) | |
88 } else { | |
89 txi_out <- tximport(files, type=opt$format, tx2gene=tx2gene,countsFromAbundance=opt$countsFromAbundance) | |
90 } | |
91 } else { # the gene_ID is a column in the counts table | |
92 if (opt$format == 'none'){ #predefined format | |
93 txi_out <- tximport(files, type="none",geneIdCol=opt$geneIdCol,txIdCol=opt$txIdCol,abundanceCol=opt$abundanceCol,countsCol=opt$countsCol,lengthCol=opt$lengthCol,tx2gene=tx2gene,countsFromAbundance=opt$countsFromAbundance) | |
94 } else { | |
95 txi_out <- tximport(files, type=opt$format, geneIdCol=opt$geneIdCol,countsFromAbundance=opt$countsFromAbundance) | |
96 } | |
97 | |
98 } | |
99 # write count as table | |
100 write.table(txi_out$counts, file=opt$out_file, row.names = TRUE, col.names = TRUE, quote = FALSE, sep = "\t") |