library("tximport")

suppressPackageStartupMessages(library("AnnotationDbi"))

tx <- GenomicFeatures::makeTxDbFromGFF(file = snakemake@input$gtf,

format = "gtf",

organism = snakemake@params$animal)

k <- AnnotationDbi::keys(tx, keytype = "GENEID")

tx_df <- AnnotationDbi::select(tx,

keys = k,

keytype = "GENEID",

columns = "TXNAME")

tx2gene <- tx_df[, 2:1]

txi <- tximport::tximport(snakemake@input$file,

type = snakemake@params$method,

tx2gene = tx2gene,

ignoreTxVersion = TRUE)

colnames(txi$counts) <- snakemake@wildcards$SRR_ID

txi$counts <- round(txi$counts)

df <- data.frame(txi$counts)

data.table::setDT(df, keep.rownames = "gene_id")

fname <- paste(snakemake@wildcards$BASE, "deseq2", "counts",

snakemake@wildcards$SRR_ID, sep = "/")

fname <- paste0(fname, "/", snakemake@wildcards$SRR_ID, ".",

snakemake@params$method, ".counts")

write.csv(df, file = fname, row.names = FALSE)