[Seqinr-commits] r1826 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Nov 27 12:05:49 CET 2014
Author: simonpenel
Date: 2014-11-27 12:05:49 +0100 (Thu, 27 Nov 2014)
New Revision: 1826
Modified:
pkg/man/draw.oriloc.Rd
pkg/man/draw.rearranged.oriloc.Rd
pkg/man/extract.breakpoints.Rd
pkg/man/gb2fasta.Rd
pkg/man/gbk2g2.Rd
pkg/man/oriloc.Rd
pkg/man/read.fasta.Rd
pkg/man/rearranged.oriloc.Rd
Log:
Now acces to voluminous data is done via ftp, changing examples
Modified: pkg/man/draw.oriloc.Rd
===================================================================
--- pkg/man/draw.oriloc.Rd 2014-11-27 11:04:53 UTC (rev 1825)
+++ pkg/man/draw.oriloc.Rd 2014-11-27 11:05:49 UTC (rev 1826)
@@ -48,6 +48,7 @@
\code{\link{extract.breakpoints}} }
\examples{
+\dontrun{ # need internet connection
#
# Example with Chlamydia trachomatis complete genome
#
@@ -62,7 +63,7 @@
cg.mtext = "CG skew", cg.col = "blue",
cds.mtext = "CDS skew", cds.col = "seagreen",
add.grid = FALSE)
-
}
+}
\keyword{hplot}
Modified: pkg/man/draw.rearranged.oriloc.Rd
===================================================================
--- pkg/man/draw.rearranged.oriloc.Rd 2014-11-27 11:04:53 UTC (rev 1825)
+++ pkg/man/draw.rearranged.oriloc.Rd 2014-11-27 11:05:49 UTC (rev 1826)
@@ -45,9 +45,14 @@
### 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", 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",
g2.coord = system.file("sequences/ct.coord", package = "seqinr"))
+
+
### Extract the breakpoints for the rearranged nucleotide skews ###
breaks <- extract.breakpoints(r.ori, type = c("gcfw", "gcrev"),
Modified: pkg/man/extract.breakpoints.Rd
===================================================================
--- pkg/man/extract.breakpoints.Rd 2014-11-27 11:04:53 UTC (rev 1825)
+++ pkg/man/extract.breakpoints.Rd 2014-11-27 11:05:49 UTC (rev 1826)
@@ -70,7 +70,7 @@
### Rearrange the chromosome and compute the nucleotide skews ###
-\dontrun{r.ori <- rearranged.oriloc(seq.fasta = system.file("sequences/ct.fasta",package = "seqinr"),
+\dontrun{r.ori <- rearranged.oriloc(seq.fasta = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta",
g2.coord = system.file("sequences/ct.coord",package = "seqinr"))}
### Extract the breakpoints for the rearranged nucleotide skews ###
Modified: pkg/man/gb2fasta.Rd
===================================================================
--- pkg/man/gb2fasta.Rd 2014-11-27 11:04:53 UTC (rev 1825)
+++ pkg/man/gb2fasta.Rd 2014-11-27 11:05:49 UTC (rev 1826)
@@ -25,6 +25,6 @@
\author{J.R. Lobry }
\seealso{ \code{\link{oriloc}} }
\examples{
-\dontrun{gb2fasta()}
+\dontrun{gb2fasta()} # need internet connection
}
\keyword{utilities}
Modified: pkg/man/gbk2g2.Rd
===================================================================
--- pkg/man/gbk2g2.Rd 2014-11-27 11:04:53 UTC (rev 1825)
+++ pkg/man/gbk2g2.Rd 2014-11-27 11:05:49 UTC (rev 1826)
@@ -7,7 +7,7 @@
glimmer program output.
}
\usage{
-gbk2g2(gbkfile = system.file("sequences/ct.gbk", package ="seqinr"),
+gbk2g2(gbkfile = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.gbk",
g2.coord = "g2.coord")
}
@@ -28,9 +28,11 @@
\seealso{ \code{\link{oriloc}} which uses glimmer-like files,
\code{\link{gbk2g2.euk}} for eukaryotic sequences with introns.}
\examples{
- suppressWarnings(gbk2g2(g2.coord = "gbk2g2.test"))
- res <- read.table("gbk2g2.test")
- head(res)
- stopifnot(nrow(res) == 892)
+ \dontrun{ # need internet connection
+ suppressWarnings(gbk2g2(g2.coord = "gbk2g2.test"))
+ res <- read.table("gbk2g2.test")
+ head(res)
+ stopifnot(nrow(res) == 892)
+ }
}
\keyword{utilities}
Modified: pkg/man/oriloc.Rd
===================================================================
--- pkg/man/oriloc.Rd 2014-11-27 11:04:53 UTC (rev 1825)
+++ pkg/man/oriloc.Rd 2014-11-27 11:05:49 UTC (rev 1826)
@@ -7,17 +7,16 @@
between codon positions.
}
\usage{
-oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
- g2.coord = system.file("sequences/ct.predict", package = "seqinr"),
+oriloc(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, clean.tmp.files = TRUE, rot = 0)
}
\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
- to use the fasta file \code{ct.fasta} which is distributed in the
- \code{sequences} folder in the seqinR package. This is the file
+ \code{ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta}, is
+ to use the fasta file \code{ct.fasta} which is available at the on the pbil server. 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
@@ -138,7 +137,7 @@
#
# Example with a single GenBank file:
#
-out2 <- oriloc(gbk=system.file("sequences/ct.gbk", package = "seqinr"))
+out2 <- oriloc(gbk="ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.gbk")
draw.oriloc(out2)
#
# (some warnings are generated because of join in features and a gene that
Modified: pkg/man/read.fasta.Rd
===================================================================
--- pkg/man/read.fasta.Rd 2014-11-27 11:04:53 UTC (rev 1825)
+++ pkg/man/read.fasta.Rd 2014-11-27 11:05:49 UTC (rev 1826)
@@ -7,7 +7,7 @@
Read nucleic or amino-acid sequences from a file in FASTA format.
}
\usage{
-read.fasta(file = system.file("sequences/ct.fasta", package = "seqinr"),
+read.fasta(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$sizeof.longlong,
@@ -150,8 +150,9 @@
# Example of a MAQ binary fasta file produced with maq fasta2bfa ct.fasta ct.bfa
# on a platform where .Platform$endian == "little" and .Machine$sizeof.longlong == 8
#
- fastafile <- system.file("sequences/ct.fasta", package = "seqinr")
- bfafile <- system.file("sequences/ct.bfa", package = "seqinr")
+\dontrun{
+ fastafile <- "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta"
+ bfafile <- "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.bfa"
original <- read.fasta(fastafile, as.string = TRUE, set.att = FALSE)
bfavers <- read.fasta(bfafile, as.string = TRUE, set.att = FALSE, bfa = TRUE,
@@ -160,4 +161,5 @@
warning(paste("trouble reading bfa file with endian =", .Platform$endian,
"and sizeof.longlong =", .Machine$sizeof.longlong))
}
+ }
}
Modified: pkg/man/rearranged.oriloc.Rd
===================================================================
--- pkg/man/rearranged.oriloc.Rd 2014-11-27 11:04:53 UTC (rev 1825)
+++ pkg/man/rearranged.oriloc.Rd 2014-11-27 11:05:49 UTC (rev 1826)
@@ -8,13 +8,13 @@
}
\usage{rearranged.oriloc(
- 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" )}
\arguments{
\item{seq.fasta}{The path of the file containing a FASTA-format
- sequence. Default value: system.file("sequences/ct.fasta",package =
- "seqinr") - the FASTA sequence of the Chlamydia trachomatis chromosome. }
+ sequence. Default value: "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta"
+ - 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 =
- system.file("sequences/ct.fasta",package = "seqinr"),
- g2.coord = system.file("sequences/ct.coord",package = "seqinr"))}
+ "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.fasta",
+ g2.coord = "ftp://pbil.univ-lyon1.fr/pub/seqinr/data/ct.coord")}
### Extract the breakpoints for the rearranged nucleotide skews ###
More information about the Seqinr-commits
mailing list