Browse code

Fixed jaspar format spacing and updated DESCRIPTION

Matthew Richards authored on 18/09/2017 18:31:33
Showing4 changed files

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@@ -1,14 +1,14 @@
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 Package: MotifDb
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 Type: Package
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 Title: An Annotated Collection of Protein-DNA Binding Sequence Motifs
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-Version: 1.19.7
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-Date: 2017-09-12
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+Version: 1.19.8
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+Date: 2017-09-18
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 Author: Paul Shannon, Matt Richards
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 Maintainer: Paul Shannon <pshannon@systemsbiology.org>
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 Depends: R (>= 2.15.0), methods, BiocGenerics, S4Vectors, IRanges, Biostrings
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 Suggests: RUnit, seqLogo, MotIV
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-Imports: rtracklayer
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-Description: More than 2000 annotated position frequency matrices from nine public sources, for multiple organisms.
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+Imports: rtracklayer, splitstackshape
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+Description: More than 8000 annotated position frequency matrices from 13 public sources, for multiple organisms.
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 License: Artistic-2.0 | file LICENSE
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 License_is_FOSS: no
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 License_restricts_use: yes
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@@ -335,7 +335,10 @@ matrixToJasparText <- function (matrices)
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       s[index] <- ""
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       index <- index + 1
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-    } # for name
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+  } # for name
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+
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+  # Remove the last blank line
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+  s <- s[-length(s)]
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   invisible (s)
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@@ -2,7 +2,9 @@ library (MotifDb)
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 library (RUnit)
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 library (MotIV)
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 library (seqLogo)
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-#------------------------------------------------------------------------------------------------------------------------
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+#----------------------------------------------------------------------------------------------------
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+printf <- function(...) print(noquote(sprintf(...)))
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+#----------------------------------------------------------------------------------------------------
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 runTests = function ()
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 {
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   test.emptyCtor ()
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@@ -121,7 +123,9 @@ test.noNAorganisms = function ()
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 {
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   print ('--- test.noNAorganisms')
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   #checkEquals (which (is.na (mcols(MotifDb)$organism)), integer (0))
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-  checkEquals(sum(is.na (mcols(MotifDb)$organism)), 1050)
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+
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+  # There's a fair number of NA organisms, mostly due to including the homer DB
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+  checkEquals(sum(is.na (mcols(MotifDb)$organism)), 366)
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 } # test.noNAorganisms
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 #------------------------------------------------------------------------------------------------------------------------
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deleted file mode 100644
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-hi