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3
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1 library(getopt)
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2
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3 # we read the options from the default: commandArgs(TRUE).
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4 spec <- matrix(c(
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5 "input_type", "t", 1, "character",
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6 "outfile", "o", 1, "character",
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7 "gtfFile", "x", 1, "character"),
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8 byrow=TRUE, ncol=4)
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9 opt <- getopt(spec)
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10
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11 suppressPackageStartupMessages({library("GenomicFeatures")})
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12 txdb <- makeTxDbFromGFF(opt$gtfFile, format=opt$input_type)
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13 k <- keys(txdb, keytype = "GENEID")
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14 df <- select(txdb, keys = k, keytype = "GENEID", columns = "TXNAME")
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15 tx2gene <- df[, 2:1] # tx ID, then gene ID
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16 write.table(tx2gene,file = opt$outfile, quote = FALSE, sep = " ",row.names = FALSE,col.names = FALSE)
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17
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