8000 wrong output file path is checked for existence · Issue #358 · al2na/methylKit · GitHub
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alexg9010 opened this issue Apr 16, 2025 · 0 comments
Open

wrong output file path is checked for existence #358

alexg9010 opened this issue Apr 16, 2025 · 0 comments
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alexg9010 commented Apr 16, 2025 •
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The output file is currently assumed in the same folder as the input tabix file. This is violated if dbdir argument is given.
The file is created at the correct path though.

methylKit/R/methylDBFunctions.R

Lines 2273 to 2294 in ecf8584

# catch additional args
args <- list(...)
dir <- dirname(object@dbpath)
if( "dbdir" %in% names(args) ){
if( !(is.null(args$dbdir)) ){
dir <- .check.dbdir(args$dbdir)
}
}
if(!( "suffix" %in% names(args) ) ){
suffix <- "_tiled"
} else {
suffix <- paste0("_",args$suffix)
}
# filename <- paste0(paste(object@sample.id,collapse = "_"),
# suffix,".txt")
filename <- paste0(gsub(".txt.bgz","",object@dbpath),suffix,".txt")
filename <- .checkTabixFileExists(filename)

Simple test:

library(methylKit)
data("methylKit")

dbdir <- "my_storage_path"
dbdir_unite <- file.path(dbdir,"unite")
dbdir_tile <- file.path(dbdir,"tile")
dbdir_diffmeth <- file.path(dbdir,"diffmeth")


## init methylrawlistdb in old dbdir
mlist_db <- methylRawList.obj |> makeMethylDB(dbdir = dbdir)
mlist_db |> getDBPath() |> basename() %in% dir(dbdir) |> all()


get_checked_file <- function(log) {
  matches <- log |> grep(pattern = "checking wether tabix file already exists:" ) + 1 
  return(log[matches])
}

## create new methylbase in new dbdir
unite_log <- {mlist_db_unite <- mlist_db |> unite(dbdir = dbdir_unite)} |> capture.output(type = "message")
identical(
  unite_log |> get_checked_file() |> normalizePath(),
  mlist_db_unite |> getDBPath()
  )

## prints the wrong for diffmeth
diffmeth_log <- {mlist_db_diffmeth <- mlist_db_unite |> calculateDiffMeth(dbdir = dbdir_diffmeth)} |> capture.output(type = "message")
identical(
  diffmeth_log |> get_checked_file() |> normalizePath(),
  mlist_db_diffmeth |> getDBPath()
)


## prints the wrong for tiling
tile_log <- {mlist_db_tiled <- mlist_db |> tileMethylCounts(dbdir = dbdir_tile)} |> capture.output(type = "message") 
identical(
  tile_log |> get_checked_file() |> normalizePath(),
  mlist_db_tiled |> getDBPath()
)


unlink(x = c(dbdir), recursive = TRUE)
@alexg9010 alexg9010 self-assigned this Apr 16, 2025
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