@@ -164,7 +164,7 @@ setMethod ('export',  signature=c(object='MotifList', con='connection',

   function (object, con, format, ...) {

-    fmt = match.arg (tolower (format), c ('meme', 'transfac'))

+    fmt = match.arg (tolower (format), c ('meme', 'transfac','jaspar'))

     ## match.arg fails if !fmt %in% c('meme', 'transfac'), so no need

     ## for test

     ## let the user manage opened cons

@@ -172,10 +172,14 @@ setMethod ('export',  signature=c(object='MotifList', con='connection',

         open(con)

         on.exit(close(con))

     }

-    if (fmt == 'meme') 

-      text = matrixToMemeText (object)

+    if (fmt == 'meme') {

+        text = matrixToMemeText (object)

+    } else if (fmt == 'jaspar') {

+        text = matrixToJasparText (object)

+    }

     cat (text, sep='\n', file=con)

-    })

+  })

+

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

 # write to connection, using default format,  ??? for matrix list, tsv for

@@ -185,13 +189,18 @@ setMethod ('export',  signature=c(object='MotifList',  con='missing',

   function (object, con, format,  ...) {

-    fmt = match.arg (tolower (format), c ('meme')) # , 'transfac'

+    fmt = match.arg (tolower (format), c ('meme','jaspar')) # , 'transfac'

     if (fmt == 'meme') {

-      text = paste (matrixToMemeText (object), collapse='\n')

+        text = paste (matrixToMemeText (object), collapse='\n')

       cat (text)

       invisible (text)

-      }

-    })

+    } else if (fmt == 'jaspar') {

+        text = paste (matrixToJasparText (object), collapse='\n')

+      cat (text)

+      invisible (text)

+    }

+      

+  })

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

 setMethod('show', 'MotifList',

@@ -262,3 +271,61 @@ setMethod ('query', 'MotifList',

         object [indices]

       })

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

+# Addition on 2017/06/15 from Matt Richards

+

+# This will not exactly match JASPAR because units are PFM and JASPAR uses PCM

+# General JASPAR Format:

+

+# > "Motif Name"\t"Transcription Factor"

+# A [ PCMS ]

+# C [ PCMS ]

+# G [ PCMS ]

+# T [ PCMS ]

+#

+# ...

+

+# Note: the PCMs are space-delimited

+

+matrixToJasparText <- function (matrices)

+{

+  matrix.count <- length (matrices)

+

+  # Incoming matrices have nucleotide rows, position columns.

+  # This is the correct orientation for JASPAR; however, we need to also

+  # add brackets and letters to them

+

+  # Calculate the number of lines of text by counting matrices and assuming

+  # 6 lines per matrix

+  

+  predicted.line.count <- 6*matrix.count

+

+  #s = vector ('character', predicted.line.count)

+  s <- character (predicted.line.count)

+

+  index <- 1

+  

+  for (name in names (matrices)) {

+

+      # Print the name with an arrow, follwed by the motif

+      s[index] <- sprintf('>%s',name)

+      index <- index + 1

+

+      # For each line of the matrix, print the correct letter and the

+      # matrix row surrounded by brackets

+      motif.matrix <- matrices[name][[1]]

+      for (r in 1:nrow(motif.matrix)) {

+          s[index] <- sprintf("%s [ %s ]",

+                              rownames(motif.matrix)[r],

+                              paste(motif.matrix[r,],collapse=" "))

+          index <- index + 1

+      }

+

+      s[index] <- ""

+      index <- index + 1

+          

+    } # for name

+

+  invisible (s)

+

+} # matrixToJasparText

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

@@ -36,6 +36,8 @@ run.tests = function ()

   test.MotIV.toTable ()

   test.run_MotIV.motifMatch()

   test.flyFactorGeneSymbols()

+  test.export_jasparFormatStdOut ()

+  test.export_jasparFormatToFile ()

 } # run.tests

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

@@ -697,4 +699,33 @@ test.flyFactorGeneSymbols <- function()

 } # test.flyFactorGeneSymbols

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

+test.export_jasparFormatStdOut = function ()

+{

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

+  mdb = MotifDb # ()

+  mdb.chicken = subset (mdb, organism=='Gallus')

+  checkEquals (length (mdb.chicken), 3)

+    # text is cat-ed to stdout, so not avaialable here to check.

+    # but just like print, export also returns the text invisibly.

+    # so that CAN be checked.

+  

+  jaspar.text = export (mdb.chicken, format='jaspar')

+  checkEquals (length (jaspar.text), 1)   # just one long string

+  checkTrue (is.character (jaspar.text))

+  checkTrue (nchar (jaspar.text) > 800)   # 1002 as of (10 aug 2012)

+  return (TRUE)

+

+} # test.exportjasparFormatToStdOut

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

+test.export_jasparFormatToFile = function ()

+{

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

+  mdb = MotifDb # ()

+  mdb.chicken = subset (mdb, organism=='Gallus')

+  checkEquals (length (mdb.chicken), 3)

+  output.file = tempfile ()

+  jaspar.text = export (mdb.chicken, output.file, 'jaspar')

+  retrieved = scan (output.file, what=character (0), sep='\n', quiet=TRUE)

+  invisible (retrieved)

+} # test.exportjasparFormatToFile