[Seqinr-commits] r1887 - www/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 2 11:26:12 CEST 2016
Author: jeanlobry
Date: 2016-06-02 11:26:12 +0200 (Thu, 02 Jun 2016)
New Revision: 1887
Modified:
www/src/mainmatter/getseqflat.rnw
www/src/mainmatter/getseqflat.tex
Log:
updating file names
Modified: www/src/mainmatter/getseqflat.rnw
===================================================================
--- www/src/mainmatter/getseqflat.rnw 2016-06-02 09:22:42 UTC (rev 1886)
+++ www/src/mainmatter/getseqflat.rnw 2016-06-02 09:26:12 UTC (rev 1887)
@@ -140,7 +140,7 @@
<<oriloc, fig=TRUE, results = hide, eval=T>>=
out <- oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
- g2.coord = system.file("sequences/ct.coord", package = "seqinr"),
+ g2.coord = system.file("sequences/ct.predict", package = "seqinr"),
oldoriloc = TRUE)
plot(out$st, out$sk/1000, type="l", xlab = "Map position in Kb",
ylab = "Cumulated composite skew in Kb",
@@ -159,7 +159,7 @@
<<oriloc2, fig=TRUE, results = hide, eval=T>>=
out <- oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
- g2.coord = system.file("sequences/ct.coord", package = "seqinr"))
+ g2.coord = system.file("sequences/ct.predict", package = "seqinr"))
plot(out$st, out$sk/1000, type="l", xlab = "Map position in Kb",
ylab = "Cumulated composite skew in Kb",
main = expression(italic(Chlamydia~~trachomatis)~~complete~~genome), las = 1)
Modified: www/src/mainmatter/getseqflat.tex
===================================================================
--- www/src/mainmatter/getseqflat.tex 2016-06-02 09:22:42 UTC (rev 1886)
+++ www/src/mainmatter/getseqflat.tex 2016-06-02 09:26:12 UTC (rev 1887)
@@ -67,11 +67,11 @@
list.files(path = system.file("sequences", package = "seqinr"), pattern = ".fasta")
\end{Sinput}
\begin{Soutput}
- [1] "Anouk.fasta" "bb.fasta" "bordetella.fasta"
- [4] "ct.fasta" "DarrenObbard.fasta" "ecolicgpe5.fasta"
- [7] "gopher.fasta" "humanMito.fasta" "legacy.fasta"
-[10] "louse.fasta" "malM.fasta" "ortho.fasta"
-[13] "seqAA.fasta" "smallAA.fasta"
+ [1] "Anouk.fasta" "bordetella.fasta" "ct.fasta"
+ [4] "DarrenObbard.fasta" "ecolicgpe5.fasta" "gopher.fasta"
+ [7] "humanMito.fasta" "legacy.fasta" "louse.fasta"
+[10] "malM.fasta" "ortho.fasta" "seqAA.fasta"
+[13] "smallAA.fasta"
\end{Soutput}
\end{Schunk}
@@ -396,7 +396,7 @@
\begin{Schunk}
\begin{Sinput}
out <- oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
- g2.coord = system.file("sequences/ct.coord", package = "seqinr"),
+ g2.coord = system.file("sequences/ct.predict", package = "seqinr"),
oldoriloc = TRUE)
plot(out$st, out$sk/1000, type="l", xlab = "Map position in Kb",
ylab = "Cumulated composite skew in Kb",
@@ -418,7 +418,7 @@
\begin{Schunk}
\begin{Sinput}
out <- oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
- g2.coord = system.file("sequences/ct.coord", package = "seqinr"))
+ g2.coord = system.file("sequences/ct.predict", package = "seqinr"))
plot(out$st, out$sk/1000, type="l", xlab = "Map position in Kb",
ylab = "Cumulated composite skew in Kb",
main = expression(italic(Chlamydia~~trachomatis)~~complete~~genome), las = 1)
@@ -472,7 +472,7 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 3.766 0.022 3.789
+ 3.790 0.034 3.824
\end{Soutput}
\end{Schunk}
@@ -493,7 +493,7 @@
\end{Sinput}
\begin{Soutput}
user system elapsed
- 0.151 0.001 0.153
+ 0.164 0.002 0.165
\end{Soutput}
\end{Schunk}
@@ -1263,15 +1263,20 @@
example(read.alignment)
\end{Sinput}
\begin{Soutput}
-rd.lgn mase.res <- read.alignment(file = system.file("sequences/test.mase", package = "seqinr"), format = "mase")
+rd.lgn mase.res <- read.alignment(file = system.file("sequences/test.mase", package = "seqinr"),
+rd.lgn format = "mase")
-rd.lgn clustal.res <- read.alignment(file = system.file("sequences/test.aln", package = "seqinr"), format="clustal")
+rd.lgn clustal.res <- read.alignment(file = system.file("sequences/test.aln", package = "seqinr"),
+rd.lgn format="clustal")
-rd.lgn phylip.res <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"), format = "phylip")
+rd.lgn phylip.res <- read.alignment(file = system.file("sequences/test.phylip", package = "seqinr"),
+rd.lgn format = "phylip")
-rd.lgn msf.res <- read.alignment(file = system.file("sequences/test.msf", package = "seqinr"), format = "msf")
+rd.lgn msf.res <- read.alignment(file = system.file("sequences/test.msf", package = "seqinr"),
+rd.lgn format = "msf")
-rd.lgn fasta.res <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"), format = "fasta")
+rd.lgn fasta.res <- read.alignment(file = system.file("sequences/Anouk.fasta", package = "seqinr"),
+rd.lgn format = "fasta")
rd.lgn #
rd.lgn # Quality control routine sanity checks:
@@ -1513,20 +1518,20 @@
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}\raggedright
- \item R version 3.1.0 (2014-04-10), \verb|x86_64-apple-darwin13.1.0|
+ \item R version 3.2.4 (2016-03-10), \verb|x86_64-apple-darwin13.4.0|
\item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/fr_FR.UTF-8/fr_FR.UTF-8|
\item Base packages: base, datasets, graphics, grDevices, grid,
methods, stats, utils
- \item Other packages: ade4~1.6-2, ape~3.1-2, grImport~0.9-0,
- MASS~7.3-31, seqinr~3.0-11, tseries~0.10-32, XML~3.98-1.1,
- xtable~1.7-3
- \item Loaded via a namespace (and not attached): lattice~0.20-29,
- nlme~3.1-117, quadprog~1.5-5, tools~3.1.0, zoo~1.7-11
+ \item Other packages: ade4~1.7-4, ape~3.5, grImport~0.9-0,
+ MASS~7.3-45, seqinr~3.1-5, tseries~0.10-35, XML~3.98-1.4,
+ xtable~1.8-2
+ \item Loaded via a namespace (and not attached): lattice~0.20-33,
+ nlme~3.1-125, quadprog~1.5-5, tools~3.2.4, zoo~1.7-12
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Fri Jun 6 18:34:24 2014
+ \item \Rlogo{} compilation time was: Thu Jun 2 11:16:34 2016
\item \LaTeX{} compilation time was: \today
\end{itemize}
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