@@ -94,7 +94,6 @@ parsePWMfromText = function (lines.of.text)

 {

   stopifnot (sum (sapply (c ('A', 'C', 'T', 'G'), function (token) length (grep (token, lines.of.text)))) == 4)

-

   for (line in lines.of.text) {

     tokens = strsplit (line, '\\s*[:\\|]') [[1]]

     nucleotide = tokens [1]

@@ -118,11 +117,10 @@ readAndParse = function (filenames)

   matrices = list ()

   for (filename in filenames) {

-    lines.of.text = scan (filename, what=character(0), sep='\n', comment='#', quiet=TRUE)

-    mtx = parsePWMfromText (lines.of.text)

-    #mtx.normalized = apply (mtx, 2, function (colvector) colvector / sum (colvector))

-    matrices [[basename(filename)]] = mtx

-    }

+      lines.of.text = scan (filename, what=character(0), sep='\n', comment='#', quiet=TRUE)

+      mtx = parsePWMfromText (lines.of.text)

+      matrices [[basename(filename)]] = mtx

+       }

    invisible (matrices)

@@ -4,7 +4,10 @@ library (RUnit)

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

 source("import.R")

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

-run.tests = function (flyFactorSurveyRootDir="~/s/data/public/TFBS/flyFactorSurvey/unpacked")

+#kDataDir <- "~/s/data/public/TFBS/flyFactorSurvey/unpacked"

+kDataDir <- "/shared/silo_researcher/Morgan_M/BioC/MotifDb/flyFactorSurvey"

+#-------------------------------------------------------------------------------

+run.tests = function (flyFactorSurveyRootDir=kDataDir)

 {

     freshStart ()

     test.fbgnToIDs()

@@ -60,10 +63,11 @@ test.getMatrixFilenames = function (flyFactorSurveyRootDir)

        # as of (03 apr 2013): 614 matrix files, one binding domains extra

        # file, TFfile2b.tsv

-    checkEquals (length (filenames), 615)

-    checkEquals(filenames[1:3],

-                c("Abd-A_FlyReg_FBgn0000014.pfm", "Abd-B_FlyReg_FBgn0000015.pfm",

-                  "AbdA_Cell_FBgn0000014.pfm"))

+    checkTrue(length (filenames) > 600)

+    sample.files <- c("Abd-A_FlyReg_FBgn0000014.pfm", "Abd-B_FlyReg_FBgn0000015.pfm",

+                      "AbdA_Cell_FBgn0000014.pfm")

+    checkTrue(all(sample.files %in% filenames))

+

     invisible (filenames)

 } # test.getMatrixFilenames

@@ -81,8 +85,9 @@ test.createExperimentRefTable = function ()

 test.parsePWMfromText = function (flyFactorSurveyRootDir)

 {

     print ('--- test.parsePWMfromText')

-    path <- file.path(flyFactorSurveyRootDir, 'Tup_SOLEXA_10_FBgn0003896.pfm')

-

+    path <- file.path(flyFactorSurveyRootDir, 'tup_SOLEXA_10_FBgn0003896.pfm')

+    checkTrue(file.exists(path))

+    

     lines.of.text =  scan (path, sep='\n',

                            what=character(0), comment='#', quiet=TRUE)

     pwm.tup =  parsePWMfromText (lines.of.text)

@@ -101,8 +106,12 @@ test.readAndParse = function (flyFactorSurveyRootDir)

     all.files = file.path(flyFactorSurveyRootDir,

                           getMatrixFilenames (flyFactorSurveyRootDir))

-    sample.files = all.files [1:3]   # grep ('FBgn0003896', all.files)

-    checkEquals (length (sample.files), 3)

+    sample.files <- c("Abd-A_FlyReg_FBgn0000014.pfm",

+                      "Abd-B_FlyReg_FBgn0000015.pfm",

+                      "AbdA_Cell_FBgn0000014.pfm")

+

+    checkTrue(all(sample.files %in% list.files(flyFactorSurveyRootDir)))

+    sample.files <- file.path(flyFactorSurveyRootDir, sample.files)

     checkTrue(all(file.exists(sample.files)))

       # by sorting these filenames, we know the order of the three returned

@@ -111,6 +120,8 @@ test.readAndParse = function (flyFactorSurveyRootDir)

     mtx.test = readAndParse (sample.files)

     checkEquals (length (mtx.test), 3)

+        # names are alphabetized, and sort differently in linux and macos

+        # work around that by 

     expected.names = c("Abd-A_FlyReg_FBgn0000014.pfm",

                        "Abd-B_FlyReg_FBgn0000015.pfm",

                        "AbdA_Cell_FBgn0000014.pfm")

@@ -160,6 +171,21 @@ test.createMetadata = function (matrices, tbl.ref, xref, list.BD)

 } # test.createMetadata

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

+test.normalizeMatrices = function (matrices)

+{

+  print ('--- test.normalizeMatrices')

+

+  colsums = as.integer (sapply (matrices, function (mtx) as.integer (mean (round (colSums (mtx))))))

+  checkTrue (all (colsums > 1))

+

+  matrices.norm = normalizeMatrices (matrices)

+

+  colsums = as.integer (sapply (matrices.norm, function (mtx) as.integer (mean (round (colSums (mtx))))))

+  checkTrue (all (colsums == 1))

+  invisible (matrices.norm)

+

+} # test.normalizeMatrices

+#------------------------------------------------------------------------------------------------------------------------

 test.renameMatrices = function (matrices, tbl.md)

 {

     print ('--- test.renameMatrices')