rm feather package

tornado2047 · Mar 23, 2021 · 0e243fd · 0e243fd
1 parent 7bb897e
commit 0e243fd
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Showing 3 changed files with 21 additions and 12 deletions.
diff --git a/R/class_ScenicOptions.R b/R/class_ScenicOptions.R
@@ -472,12 +472,14 @@ dbVersion <- function(dbs)
 #' @rdname ScenicOptions-class
 #' @export 
 dbLoadingAttempt <- function(dbFilePath){
-  ret <- FALSE
-  ret <- tryCatch({
-    md <- feather::feather_metadata(dbFilePath)
-    md$path
-    md$dim[2] == length(md$types)
-    randomCol <- sample(names(md$types),1)
+    ret <- FALSE
+    ret <- tryCatch({
+    rf <- arrow::ReadableFile$create(dbFilePath)
+    fr <- arrow::FeatherReader$create(rf)
+    fr$version
+    genesInDb <- names(fr)
+    randomCol <- sample(genesInDb, 1)
+    fr$Read(randomCol)
     rnk <- RcisTarget::importRankings(dbFilePath, columns=randomCol)
     return(TRUE)
   }
@@ -497,10 +499,12 @@ checkAnnots <- function(object, motifAnnot)
   allFeaturesInAnnot <- unlist(motifAnnot[,1]) # motif or track
   featuresWithAnnot <-  lapply(getDatabases(object), function(dbFile) 
   {
-    nRnks <- unlist(feather::read_feather(dbFile, columns="features")[,1])
+    rnktype = "features"	#TODO: add as option for custom dbs
+    nRnks <- getRanking(RcisTarget::importRankings(dbFile, columns = rnktype))
+    nRnks <- dplyr::pull(nRnks, rnktype)
+
     length(intersect(allFeaturesInAnnot,nRnks))/length(unique(c(allFeaturesInAnnot,nRnks)))
   })
   return(featuresWithAnnot)
 }
 
-
diff --git a/R/runSCENIC_2_createRegulons.R b/R/runSCENIC_2_createRegulons.R
@@ -64,8 +64,13 @@ runSCENIC_2_createRegulons <- function(scenicOptions,
   if(any(!loadAttempt)) stop("It is not possible to load the following databses: \n",
                                 paste(dbs[which(!loadAttempt)], collapse="\n"))
 
-  genesInDb <- unique(unlist(lapply(getDatabases(scenicOptions), function(x)
-    names(feather::feather_metadata(x)[["types"]]))))
+  genesInDb <- unique(unlist(lapply(getDatabases(scenicOptions), function(dbFilePath) {
+	rf <- arrow::ReadableFile$create(dbFilePath)
+	fr <- arrow::FeatherReader$create(rf)
+	genesInDb <- names(fr)
+	rnktype <- "features"        #TODO: add as option for custom dbs
+	genesInDb <- genesInDb[genesInDb != rnktype]
+	})))
 
   ## Check if annotation and rankings (potentially) match:
   featuresWithAnnot <- checkAnnots(scenicOptions, motifAnnot)
@@ -208,7 +213,7 @@ runSCENIC_2_createRegulons <- function(scenicOptions,
 
   ################################################################
   # 2. Prune targets
-  msg <- paste0(format(Sys.time(), "%H:%M"), "\tRcisTarget: Prunning targets")
+  msg <- paste0(format(Sys.time(), "%H:%M"), "\tRcisTarget: Pruning targets")
   if(getSettings(scenicOptions, "verbose")) message(msg)
 
   dbNames <- getDatabases(scenicOptions)

diff --git a/R/runSCENIC_2_createRegulons_Original.R b/R/runSCENIC_2_createRegulons_Original.R
@@ -144,7 +144,7 @@
 #'   
 #'   ################################################################
 #'   # 2. Prune targets
-#'   msg <- paste0(format(Sys.time(), "%H:%M"), "\tRcisTarget: Prunning targets")
+#'   msg <- paste0(format(Sys.time(), "%H:%M"), "\tRcisTarget: Pruning targets")
 #'   if(getSettings(scenicOptions, "verbose")) message(msg)
 #'     
 #'   dbNames <- getDatabases(scenicOptions)