[Seqinr-commits] r1892 - pkg/man

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

Author: jeanlobry
Date: 2016-06-02 13:36:01 +0200 (Thu, 02 Jun 2016)
New Revision: 1892

Modified:
   pkg/man/draw.rearranged.oriloc.Rd
   pkg/man/extract.breakpoints.Rd
   pkg/man/oriloc.Rd
   pkg/man/rearranged.oriloc.Rd
Log:
using the gzipped ct.fasta.gz

Modified: pkg/man/draw.rearranged.oriloc.Rd
===================================================================
--- pkg/man/draw.rearranged.oriloc.Rd	2016-06-02 11:27:24 UTC (rev 1891)
+++ pkg/man/draw.rearranged.oriloc.Rd	2016-06-02 11:36:01 UTC (rev 1892)
@@ -45,10 +45,10 @@
 
 ### Rearrange the chromosome and compute the nucleotide skews ###
 
-#r.ori <- rearranged.oriloc(seq.fasta = system.file("sequences/ct.fasta", package = "seqinr"),
+#r.ori <- rearranged.oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", package = "seqinr"),
 #    g2.coord = system.file("sequences/ct.coord", package = "seqinr"))
 
-r.ori <- rearranged.oriloc(seq.fasta = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta",
+r.ori <- rearranged.oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", package = "seqinr"),
     g2.coord = system.file("sequences/ct.coord", package = "seqinr"))
 
 

Modified: pkg/man/extract.breakpoints.Rd
===================================================================
--- pkg/man/extract.breakpoints.Rd	2016-06-02 11:27:24 UTC (rev 1891)
+++ pkg/man/extract.breakpoints.Rd	2016-06-02 11:36:01 UTC (rev 1892)
@@ -70,7 +70,7 @@
 
 ### Rearrange the chromosome and compute the nucleotide skews ###
 
-\dontrun{r.ori <- rearranged.oriloc(seq.fasta = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta",
+\dontrun{r.ori <- rearranged.oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", package = "seqinr"),
     g2.coord = system.file("sequences/ct.coord",package = "seqinr"))}
 
 ### Extract the breakpoints for the rearranged nucleotide skews ###

Modified: pkg/man/oriloc.Rd
===================================================================
--- pkg/man/oriloc.Rd	2016-06-02 11:27:24 UTC (rev 1891)
+++ pkg/man/oriloc.Rd	2016-06-02 11:36:01 UTC (rev 1892)
@@ -7,7 +7,7 @@
 between codon positions.
 }
 \usage{
-oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
+oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", package = "seqinr"),
  g2.coord = system.file("sequences/ct.predict", package = "seqinr"),
  glimmer.version = 3,
 oldoriloc = FALSE, gbk = NULL, clean.tmp.files = TRUE, rot = 0)
@@ -15,8 +15,8 @@
 \arguments{
   \item{seq.fasta}{Character: the name of a file which contains the DNA sequence
     of a bacterial chromosome in fasta format. The default value,
-   \code{system.file("sequences/ct.fasta", package ="seqinr")} is
-    the fasta file \code{ct.fasta}. This is the file
+   \code{system.file("sequences/ct.fasta.gz", package ="seqinr")} is
+    the fasta file \code{ct.fasta.gz}. This is the file
     for the complete genome sequence of \emph{Chlamydia trachomatis}
     that was used in Frank and Lobry (2000). You can replace
     this by something like \code{seq.fasta = "myseq.fasta"} to work

Modified: pkg/man/rearranged.oriloc.Rd
===================================================================
--- pkg/man/rearranged.oriloc.Rd	2016-06-02 11:27:24 UTC (rev 1891)
+++ pkg/man/rearranged.oriloc.Rd	2016-06-02 11:36:01 UTC (rev 1892)
@@ -8,13 +8,13 @@
   }
 
 \usage{rearranged.oriloc(
-    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 =  system.file("sequences/ct.fasta.gz", package = "seqinr"),
+    g2.coord = system.file("sequences/ct.predict", package = "seqinr")}
 
 \arguments{
 \item{seq.fasta}{The path of the file containing a FASTA-format
-  sequence. Default value:  "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta"
-  - the FASTA sequence of the Chlamydia trachomatis chromosome. }
+  sequence. Default value: 
+  the FASTA sequence of the Chlamydia trachomatis chromosome. }
 \item{g2.coord}{The path of the file containing the coordinates of the
   protein coding genes found on this chromosome. This file can be
   obtained using the function \code{gbk2g2}. The format of the file is
@@ -72,8 +72,8 @@
 ### Rearrange the chromosome and compute the nucleotide skews ###
 
 \dontrun{r.ori <- rearranged.oriloc(seq.fasta = 
-   "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta",
-    g2.coord =  "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.coord")}
+   system.file("sequences/ct.fasta.gz", package = "seqinr"),
+    g2.coord =  system.file("sequences/ct.predict", package = "seqinr"))}
 
 ### Extract the breakpoints for the rearranged nucleotide skews ###