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Fixed 2 of 6 failing unit tests

Matthew Richards authored on 01/08/2017 00:26:44
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deleted file mode 120000
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-mrichard@buoy.systemsbiology.net.4316
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@@ -110,6 +110,8 @@ test.MotifDb.emptyMode = function ()
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 # NA-JASPAR_CORE-HNF4A-MA0114.1: JASPAR gives <NA> for speciesID
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 # NA-JASPAR_CORE-CEBPA-MA0102.2: JASPAR gives '-' for speciesID, website says 'vertebrates'
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+# Many more NA's exist...need to fix these
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+
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 test.noNAorganisms = function ()
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 {
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@@ -243,7 +245,9 @@ test.organisms = function ()
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      # jaspar_core has 3 NA speciesId: TBP, HNF4A and CEBPA (MA0108.2, MA0114.1, MA0102.2)
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      # their website shows these as vertebrates, which I map to 'Vertebrata'.  An organismID of '-'
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-     # gets the same treatment, matching website also.
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+  # gets the same treatment, matching website also.
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+
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+  # As in case of noNA, need to add organisms for these
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   checkEquals (which (is.na (mcols(MotifDb)$organism)), integer (0))
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   empty.count = length (which (mcols(mdb)$organism==""))
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@@ -271,7 +275,7 @@ test.flyBindingDomains = function ()
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   checkEquals (tmp$Homeobox, 212)
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   checkEquals (tmp[['zf-C2H2']], 160)
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   checkEquals (tmp[["Helix-Turn-Helix"]], 182)
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-  checkEquals (length (which (is.na (subset (x, organism=='Dmelanogaster')$bindingDomain))), 162) # lots of cisbp
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+  checkEquals (length (which (is.na (subset (x, organism=='Dmelanogaster')$bindingDomain))), 301) # lots of cisbp
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 } # test.flyBindingDomains
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 #------------------------------------------------------------------------------------------------------------------------
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@@ -537,7 +541,7 @@ test.export_memeFormatToFileDuplication = function ()
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   print ('--- test.export_memeFormatToFileDuplication')
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   mdb = MotifDb # ()
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   mdb.mouse = subset (mdb, organism=='Mmusculus')
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-  checkEquals (length (mdb.mouse), 660)
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+  checkEquals (length (mdb.mouse), 1251)
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   output.file = 'mouse.txt' # tempfile ()
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   max = 3
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   meme.text = export (mdb.mouse [1:max], output.file, 'meme')