@@ -8,7 +8,7 @@ run.tests = function (dataDir)

 {

     dataDir <- file.path(dataDir, "flyFactorSurvey")

     freshStart ()

-    #test.fbgnToIDs()

+    test.fbgnToIDs()

     x.list.BD <- test.createXrefBindingDomain (dataDir)

     x.xref <- test.createXref ()

     x.filenames <- test.getMatrixFilenames (dataDir)

@@ -234,17 +234,16 @@ test.fbgnToIDs <- function()

     checkEquals(tbl.ids$symbol, c("ro", "exd", "pdm2", "Six4", "da"))

     checkEquals(tbl.ids$geneIdType, rep("ENTREZ", 5))

-         # 0259750 is obsolete, replace by 0264442

-    tbl.ids <- fbgnToIDs("FBgn0259750")

-    checkEquals(as.list(tbl.ids),

-                list(flybase_id="FBgn0264442", symbol="ab", gene_id="34560",

-                     geneIdType="ENTREZ"))

+         # 0259750 is obsolete, replaced by 0264442

+    x <- "FBgn0259750"

+    tbl.ids <- fbgnToIDs(x)

+    checkEquals(as.character(tbl.ids[1,]), c(rep(x,3), "FLYBASE"))

        # http://flybase.org/static_pages/downloads/IDConv.html

        # FBgn0003986 	 FBgn0261930 	FBgn0261930	 vnd 

-    tbl.ids <- fbgnToIDs("FBgn0003986")

-    checkEquals(as.character(as.list(tbl.ids[1,],)),

-                c(rep("FBgn0003986", 3), "FLYBASE"))

+    x <- "FBgn0003986"

+    tbl.ids <- fbgnToIDs(x)

+    checkEquals(as.character(tbl.ids[1,]), c(rep(x, 3), "FLYBASE"))

     serializedFbgnsForTesting <- system.file(package="MotifDb", "scripts",

                                              "import", "fbgns.RData")

@@ -260,7 +259,7 @@ test.fbgnToIDs <- function()

        # what percentage of the 326 ids fail to map?  do NOT convert NAs

     tbl.ids <- fbgnToIDs(fbgns, useInputForMissingValues=FALSE)

     failure.count <- length(which(is.na(tbl.ids$flybase_id)))

-    checkEquals(failure.count, 18)

+    checkEquals(failure.count, 23)   # as of (3 feb 2014)

 } # test.fbgnToIDsp

 #-------------------------------------------------------------------------------