@@ -1,6 +1,6 @@

 library (MotifDb)

 library (RUnit)

-library (MotIV)

+#library (MotIV)

 library (seqLogo)

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

 run.tests = function ()

@@ -33,8 +33,8 @@ run.tests = function ()

   test.export_memeFormatToFile ()

   test.export_memeFormatToFileDuplication ()

   test.export_memeFormatToFile_run_tomtom ()

-  test.run_MotIV ()

-  test.MotIV.toTable ()

+  #test.run_MotIV ()

+  #test.MotIV.toTable ()

   test.flyFactorGeneSymbols()

 } # run.tests

@@ -123,7 +123,7 @@ test.allMatricesAreNormalized = function ()

   matrices = mdb@listData

     # a lenient test required by "Cparvum-UniPROBE-Cgd2_3490.UP00395" and  "Hsapiens-UniPROBE-Sox4.UP00401"

     # for reasons not yet explored.  10e-8 should be be possible

-  checkTrue (all (sapply (matrices, function (m) all (abs (colSums (m) - 1.0) < 0.02))))

+  checkTrue(all(sapply(matrices, function (m) all (abs (colSums (m) - 1.0) < 0.02))))

 } # test.allMatricesAreNormalized

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

@@ -160,9 +160,8 @@ test.geneIdsAndTypes = function ()

   checkTrue(typeCounts$ENTREZ == 2347)

   checkTrue(typeCounts$FLYBASE >= 47)

   checkTrue(typeCounts$SGD >= 629)

-  checkEquals(nrow(subset(tbl, is.na(geneIdType))), 1181)

+  checkEquals(nrow(subset(tbl, is.na(geneIdType))), 2055)

-

   empty.count = length (which (geneIds == ''))

   checkEquals (empty.count, 0)

@@ -219,7 +218,7 @@ test.longNames = function ()

   longNames = strsplit (names (mdb), '-')

   organisms = unique (sapply (longNames, '[', 1))

-  dataSources = unique (sapply (longNames, '[', 2))

+  dataSources = unique (lapply (longNames, '[', 2))

   recognized.dataSources = unique (mcols(mdb)$dataSource)

   recognized.organisms = unique (mcols(mdb)$organism)

@@ -227,7 +226,7 @@ test.longNames = function ()

     # so that it can be matched up against the 'NA' extracted from longNames just above

   na.indices = which (is.na (recognized.organisms))

   if (length (na.indices) > 0)

-  recognized.organisms [na.indices] = 'NA'

+     recognized.organisms [na.indices] = 'NA'

   checkTrue (all (organisms %in% recognized.organisms))

   checkTrue (all (dataSources %in% recognized.dataSources))

@@ -271,7 +270,7 @@ 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))), 24)

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

 } # test.flyBindingDomains

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

@@ -537,7 +536,7 @@ test.export_memeFormatToFileDuplication = function ()

   print ('--- test.export_memeFormatToFileDuplication')

   mdb = MotifDb # ()

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

-  checkEquals (length (mdb.mouse), 528)

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

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

   max = 3

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

@@ -564,11 +563,13 @@ test.export_memeFormatToFile_run_tomtom = function (max=50)

        # find similarity of motif #1 to all the motifs in mdbMany

-    cmd = sprintf ('tomtom -no-ssc -oc %s -verbosity 3 -min-overlap 5 -mi 1 -dist pearson -evalue -thresh 10 %s %s',

-                    tomtom.tmp.dir, sox4.file.path, all.human.file.path)

-    system (cmd)

-    cmd = sprintf ('open %s/tomtom.html', tomtom.tmp.dir)

-    system (cmd)

+       # cannot rely upon tomtom being present

+

+    #cmd = sprintf ('tomtom -no-ssc -oc %s -verbosity 3 -min-overlap 5 -mi 1 -dist pearson -evalue -thresh 10 %s %s',

+    #                tomtom.tmp.dir, sox4.file.path, all.human.file.path)

+    #system (cmd)

+    #cmd = sprintf ('open %s/tomtom.html', tomtom.tmp.dir)

+    #system (cmd)

     } # if interactive

 } # test.export_memeFormatToFile_run_tomtom