add src to build table counts from h5 files

src/kallisto_output2TablCnts.R

+library(tidyverse)
+library(rhdf5)
+library(tximport)
+
+# code contributed from Andrew Morgan
+read_kallisto_h5 <- function(fpath, ...) {
+  if (!requireNamespace("rhdf5", quietly=TRUE)) {
+    stop("reading kallisto results from hdf5 files requires Bioconductor package `rhdf5`")
+  }
+  counts <- rhdf5::h5read(fpath, "est_counts")
+  ids <- rhdf5::h5read(fpath, "aux/ids")
+  efflens <- rhdf5::h5read(fpath, "aux/eff_lengths")
+
+  # as suggested by https://support.bioconductor.org/p/96958/#101090
+  ids <- as.character(ids)
+
+  stopifnot(length(counts) == length(ids))
+  stopifnot(length(efflens) == length(ids))
+
+  result <- data.frame(target_id = ids,
+                       eff_length = efflens,
+                       est_counts = counts,
+                       stringsAsFactors = FALSE)
+  normfac <- with(result, (1e6)/sum(est_counts/eff_length))
+  result$tpm <- with(result, normfac*(est_counts/eff_length))
+  return(result)
+}
+
+
+setwd("/home/arnux/counts_simulation/data/SRP217588/")
+listFile = list.files(path= ".", pattern=NULL, all.files=FALSE, full.names=FALSE)
+
+h52dtf <- function(fn){
+  print(fn)
+  h5 = tximport(files = fn,
+           type = "kallisto",
+           txOut = TRUE, importer = read_kallisto_h5 )
+  return(h5$counts)
+}
+
+a = listFile %>% map(~h52dtf(.x))
+tbl_cnts = do.call("cbind", a)
+colnames(tbl_cnts) = listFile %>% str_split(pattern = ".h5", simplify = TRUE)%>% .[,1] %>% str_replace(., '-', '_' ) %>% str_replace(., '-', '_' )
+tbl_cnts= tbl_cnts %>% data.frame()
+tbl_cnts = tbl_cnts %>% rownames_to_column("gene_id")
+write_tsv(tbl_cnts, "../../src/htrsim/inst/extdata/SRP217588.tsv" )
+#write_tsv(tbl_cnts, "../../src/htrsim/inst/extdata/SRP217588.tsv" )
+
+