[Seqinr-commits] r1895 - www/src/mainmatter

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

Author: jeanlobry
Date: 2016-06-02 14:00:10 +0200 (Thu, 02 Jun 2016)
New Revision: 1895

Modified:
   www/src/mainmatter/getseqflat.rnw
   www/src/mainmatter/getseqflat.tex
Log:
using ct.fasta.gz

Modified: www/src/mainmatter/getseqflat.rnw
===================================================================
--- www/src/mainmatter/getseqflat.rnw	2016-06-02 11:55:59 UTC (rev 1894)
+++ www/src/mainmatter/getseqflat.rnw	2016-06-02 12:00:10 UTC (rev 1895)
@@ -133,13 +133,13 @@
 
 \subsubsection{Oriloc example (\textit{Chlamydia trachomatis} complete genome)}
 
-A more consequent example is given in the fasta file \texttt{ct.fasta} which
+A more consequent example is given in the fasta file \texttt{ct.fasta.gz} which
 contains the complete genome of \textit{Chlamydia trachomatis} that was
 used in \cite{oriloc}. You should be able to reproduce figure 1b from this
 paper with the following code:
 
 <<oriloc, fig=TRUE, results = hide, eval=T>>=
-out <- oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
+out <- oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", 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",
@@ -158,7 +158,7 @@
 for a recent review on this topic.
 
 <<oriloc2, fig=TRUE, results = hide, eval=T>>=
-out <- oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
+out <- oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", 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", 

Modified: www/src/mainmatter/getseqflat.tex
===================================================================
--- www/src/mainmatter/getseqflat.tex	2016-06-02 11:55:59 UTC (rev 1894)
+++ www/src/mainmatter/getseqflat.tex	2016-06-02 12:00:10 UTC (rev 1895)
@@ -67,11 +67,11 @@
  list.files(path = system.file("sequences", package = "seqinr"), pattern = ".fasta")
 \end{Sinput}
 \begin{Soutput}
- [1] "Anouk.fasta"        "bordetella.fasta"   "ct.fasta"          
+ [1] "Anouk.fasta"        "bordetella.fasta"   "ct.fasta.gz"       
  [4] "DarrenObbard.fasta" "ecolicgpe5.fasta"   "gopher.fasta"      
  [7] "humanMito.fasta"    "legacy.fasta"       "louse.fasta"       
 [10] "malM.fasta"         "ortho.fasta"        "seqAA.fasta"       
-[13] "smallAA.fasta"     
+[13] "smallAA.fasta"      "smallAA.fasta.gz"  
 \end{Soutput}
 \end{Schunk}
 
@@ -388,14 +388,14 @@
 
 \subsubsection{Oriloc example (\textit{Chlamydia trachomatis} complete genome)}
 
-A more consequent example is given in the fasta file \texttt{ct.fasta} which
+A more consequent example is given in the fasta file \texttt{ct.fasta.gz} which
 contains the complete genome of \textit{Chlamydia trachomatis} that was
 used in \cite{oriloc}. You should be able to reproduce figure 1b from this
 paper with the following code:
 
 \begin{Schunk}
 \begin{Sinput}
- out <- oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
+ out <- oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", 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",
@@ -417,7 +417,7 @@
 
 \begin{Schunk}
 \begin{Sinput}
- out <- oriloc(seq.fasta = system.file("sequences/ct.fasta", package ="seqinr"),
+ out <- oriloc(seq.fasta = system.file("sequences/ct.fasta.gz", 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", 
@@ -472,7 +472,7 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
-  3.790   0.034   3.824 
+  3.822   0.031   3.851 
 \end{Soutput}
 \end{Schunk}
 
@@ -493,7 +493,7 @@
 \end{Sinput}
 \begin{Soutput}
    user  system elapsed 
-  0.164   0.002   0.165 
+  0.158   0.002   0.159 
 \end{Soutput}
 \end{Schunk}
 
@@ -1531,7 +1531,7 @@
 There were two compilation steps:
 
 \begin{itemize}
-  \item \Rlogo{} compilation time was: Thu Jun  2 11:16:34 2016
+  \item \Rlogo{} compilation time was: Thu Jun  2 13:57:06 2016
   \item \LaTeX{} compilation time was: \today
 \end{itemize}