deleted file mode 120000

@@ -1 +0,0 @@

-mrichard@buoy.systemsbiology.net.4316

\ No newline at end of file

@@ -110,6 +110,8 @@ test.MotifDb.emptyMode = function ()

 # NA-JASPAR_CORE-HNF4A-MA0114.1: JASPAR gives <NA> for speciesID

 # NA-JASPAR_CORE-CEBPA-MA0102.2: JASPAR gives '-' for speciesID, website says 'vertebrates'

+# Many more NA's exist...need to fix these

+

 test.noNAorganisms = function ()

 {

@@ -243,7 +245,9 @@ test.organisms = function ()

      # jaspar_core has 3 NA speciesId: TBP, HNF4A and CEBPA (MA0108.2, MA0114.1, MA0102.2)

      # their website shows these as vertebrates, which I map to 'Vertebrata'.  An organismID of '-'

-     # gets the same treatment, matching website also.

+  # gets the same treatment, matching website also.

+

+  # As in case of noNA, need to add organisms for these

   checkEquals (which (is.na (mcols(MotifDb)$organism)), integer (0))

   empty.count = length (which (mcols(mdb)$organism==""))

@@ -271,7 +275,7 @@ test.flyBindingDomains = function ()

   checkEquals (tmp$Homeobox, 212)

   checkEquals (tmp[['zf-C2H2']], 160)

   checkEquals (tmp[["Helix-Turn-Helix"]], 182)

-  checkEquals (length (which (is.na (subset (x, organism=='Dmelanogaster')$bindingDomain))), 162) # lots of cisbp

+  checkEquals (length (which (is.na (subset (x, organism=='Dmelanogaster')$bindingDomain))), 301) # lots of cisbp

 } # test.flyBindingDomains

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

@@ -537,7 +541,7 @@ test.export_memeFormatToFileDuplication = function ()

   print ('--- test.export_memeFormatToFileDuplication')

   mdb = MotifDb # ()

   mdb.mouse = subset (mdb, organism=='Mmusculus')

-  checkEquals (length (mdb.mouse), 660)

+  checkEquals (length (mdb.mouse), 1251)

   output.file = 'mouse.txt' # tempfile ()

   max = 3

   meme.text = export (mdb.mouse [1:max], output.file, 'meme')