[Seqinr-commits] r1825 - pkg/R

[noreply at r-forge.r-project.org]

Author: simonpenel
Date: 2014-11-27 12:04:53 +0100 (Thu, 27 Nov 2014)
New Revision: 1825

Modified:
   pkg/R/gbk2g2.R
   pkg/R/oriloc.R
   pkg/R/read.fasta.R
   pkg/R/rearranged.oriloc.R
Log:
Now acces to voluminous data is done via ftp, changing R code 


Modified: pkg/R/gbk2g2.R
===================================================================
--- pkg/R/gbk2g2.R	2014-11-26 13:55:16 UTC (rev 1824)
+++ pkg/R/gbk2g2.R	2014-11-27 11:04:53 UTC (rev 1825)
@@ -8,7 +8,7 @@
 #########################################################################
 
 gbk2g2 <- function(
-  gbkfile = system.file("sequences/ct.gbk", package ="seqinr"),
+  gbkfile =  "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.gbk",
   g2.coord = "g2.coord")
 {
   input <- readLines(gbkfile)

Modified: pkg/R/oriloc.R
===================================================================
--- pkg/R/oriloc.R	2014-11-26 13:55:16 UTC (rev 1824)
+++ pkg/R/oriloc.R	2014-11-27 11:04:53 UTC (rev 1825)
@@ -6,8 +6,8 @@
 ########################################################################
 
 oriloc <- function(
-  seq.fasta = system.file("sequences/ct.fasta", package = "seqinr"),
-  g2.coord = system.file("sequences/ct.predict", package = "seqinr"),
+  seq.fasta = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta",
+  g2.coord = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.predict",
   glimmer.version = 3,
   oldoriloc = FALSE,
   gbk = NULL,

Modified: pkg/R/read.fasta.R
===================================================================
--- pkg/R/read.fasta.R	2014-11-26 13:55:16 UTC (rev 1824)
+++ pkg/R/read.fasta.R	2014-11-27 11:04:53 UTC (rev 1825)
@@ -1,4 +1,4 @@
-read.fasta <- function(file = system.file("sequences/ct.fasta", package = "seqinr"), 
+read.fasta <- function(file = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta", 
   seqtype = c("DNA", "AA"), as.string = FALSE, forceDNAtolower = TRUE,
   set.attributes = TRUE, legacy.mode = TRUE, seqonly = FALSE, strip.desc = FALSE,
   bfa = FALSE, sizeof.longlong = .Machine$sizeof.longlong,

Modified: pkg/R/rearranged.oriloc.R
===================================================================
--- pkg/R/rearranged.oriloc.R	2014-11-26 13:55:16 UTC (rev 1824)
+++ pkg/R/rearranged.oriloc.R	2014-11-27 11:04:53 UTC (rev 1825)
@@ -6,8 +6,8 @@
 #############################################################################
 
 rearranged.oriloc <- function(
-    seq.fasta = system.file("sequences/ct.fasta",package = "seqinr"),
-    g2.coord = system.file("sequences/ct.coord",package = "seqinr"))
+    seq.fasta = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta" ,
+    g2.coord = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.coord" )
   {
     
     seq.fasta <- read.fasta(seq.fasta)[[1]]