[Seqinr-commits] r1483 - pkg/inst/doc/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Oct 26 18:30:17 CET 2008
Author: lobry
Date: 2008-10-26 18:30:17 +0100 (Sun, 26 Oct 2008)
New Revision: 1483
Modified:
pkg/inst/doc/src/mainmatter/getseqacnuc.tex
Log:
R 2.8.0
Modified: pkg/inst/doc/src/mainmatter/getseqacnuc.tex
===================================================================
--- pkg/inst/doc/src/mainmatter/getseqacnuc.tex 2008-10-26 17:29:24 UTC (rev 1482)
+++ pkg/inst/doc/src/mainmatter/getseqacnuc.tex 2008-10-26 17:30:17 UTC (rev 1483)
@@ -101,10 +101,10 @@
1 genbank on
2 embl on
3 emblwgs on
- info
-1 GenBank Rel. 165 (15 April 2008) Last Updated: May 12, 2008
-2 EMBL Library Release 94 (March 2008) Last Updated: May 12, 2008
-3 EMBL Whole Genome Shotgun sequences Release 94 (March 2008)
+ info
+1 GenBank Rel. 167 (15 August 2008) Last Updated: Oct 26, 2008
+2 EMBL Library Release 96 (September 2008) Last Updated: Oct 25, 2008
+3 EMBL Whole Genome Shotgun sequences Release 96 (September 2008)
\end{Soutput}
\end{Schunk}
@@ -158,16 +158,16 @@
\end{Sinput}
\begin{Soutput}
List of 9
- $ socket :Classes 'sockconn', 'connection' atomic [1:1] 6
+ $ socket :Classes 'sockconn', 'connection' atomic [1:1] 5
.. ..- attr(*, "conn_id")=<externalptr>
$ bankname: chr "genbank"
$ banktype: chr "GENBANK"
- $ totseqs : num 92540832
- $ totspecs: num 553777
- $ totkeys : num 8490208
- $ release : chr " GenBank Rel. 165 (15 April 2008) Last Updated: May 12, 2008"
+ $ totseqs : num 1.02e+08
+ $ totspecs: num 598454
+ $ totkeys : num 9391212
+ $ release : chr " GenBank Rel. 167 (15 August 2008) Last Updated: Oct 26, 2008"
$ status :Class 'AsIs' chr "on"
- $ details : chr [1:4] " **** ACNUC Data Base Content **** " " GenBank Rel. 165 (15 April 2008) Last Updated: May 12, 2008" "90,620,951,454 bases; 87,387,352 sequences; 5,153,479 subseqs; 508,578 refers." "Software by M. Gouy, Lab. Biometrie et Biologie Evolutive, Universite Lyon I "
+ $ details : chr [1:4] " **** ACNUC Data Base Content **** " " GenBank Rel. 167 (15 August 2008) Last Updated: Oct 26, 2008" "97,378,213,581 bases; 96,406,734 sequences; 5,646,527 subseqs; 525,953 refers." "Software by M. Gouy, Lab. Biometrie et Biologie Evolutive, Universite Lyon I "
\end{Soutput}
\begin{Sinput}
closebank()
@@ -177,15 +177,15 @@
The components of \texttt{banknameSocket} means that in the database
called \texttt{genbank} at the compilation time
of this document there were
-\texttt{92,540,832}
+\texttt{102,053,262}
sequences from
-\texttt{553,777}
+\texttt{598,454}
species and a total of
-\texttt{8,490,208}
+\texttt{9,391,212}
keywords. The status of the bank was
\texttt{on},
and the release information was
-\texttt{ GenBank Rel. 165 (15 April 2008) Last Updated: May 12, 2008}.
+\texttt{ GenBank Rel. 167 (15 August 2008) Last Updated: Oct 26, 2008}.
For specialized databases, some relevant informations are also given in the
\texttt{details} component, for instance:
@@ -358,17 +358,17 @@
length(ccc2004$req)
\end{Sinput}
\begin{Soutput}
-[1] 59
+[1] 60
\end{Soutput}
\begin{Sinput}
ccc2004$nelem
\end{Sinput}
\begin{Soutput}
-[1] 59
+[1] 60
\end{Soutput}
\end{Schunk}
-Hence, there were 59 complete coding sequences published in 2004 for
+Hence, there were 60 complete coding sequences published in 2004 for
\textit{Felis catus} in GenBank.
As from release 1.0-3 of the \seqinr{} package, there is new parameter \texttt{virtual}
@@ -381,15 +381,15 @@
allcds$nelem
\end{Sinput}
\begin{Soutput}
-[1] 5534531
+[1] 6067613
\end{Soutput}
\end{Schunk}
-There are therefore \texttt{5,534,531} coding
+There are therefore \texttt{6,067,613} coding
sequences in this version of GenBank\footnote{
which is stored in the \texttt{release} component of the object \texttt{banknameSocket}
and current value is today (\today): \texttt{banknameSocket\$release =
- GenBank Rel. 165 (15 April 2008) Last Updated: May 12, 2008}.
+ GenBank Rel. 167 (15 August 2008) Last Updated: Oct 26, 2008}.
}.
It would be long to get all the informations for the elements
of this list, so we have set the parameter \texttt{virtual} to \texttt{TRUE} and the \texttt{req}
@@ -416,11 +416,11 @@
small$nelem
\end{Sinput}
\begin{Soutput}
-[1] 931
+[1] 935
\end{Soutput}
\end{Schunk}
-There are then \texttt{931} elements in
+There are then \texttt{935} elements in
the list \texttt{small}, so that we can safely repeat the previous query without asking for a
virtual list:
@@ -446,10 +446,10 @@
man$nelem
\end{Sinput}
\begin{Soutput}
-[1] 11422715
+[1] 11551823
\end{Soutput}
\end{Schunk}
-There are \texttt{11,422,715} sequences from \textit{Homo sapiens}.
+There are \texttt{11,551,823} sequences from \textit{Homo sapiens}.
\item[\textbf{Sex.}] How many sequences are annotated with a keyword starting by sex?
\begin{Schunk}
@@ -458,10 +458,10 @@
sex$nelem
\end{Sinput}
\begin{Soutput}
-[1] 1323
+[1] 1346
\end{Soutput}
\end{Schunk}
-There are \texttt{1,323} such sequences.
+There are \texttt{1,346} such sequences.
\item[\textbf{tRNA.}] How many complete tRNA sequences are available?
\begin{Schunk}
@@ -470,10 +470,10 @@
trna$nelem
\end{Sinput}
\begin{Soutput}
-[1] 290961
+[1] 324327
\end{Soutput}
\end{Schunk}
-There are \texttt{290,961} complete tRNA sequences.
+There are \texttt{324,327} complete tRNA sequences.
\item[\textbf{Nature vs. Science.}] In which journal were the more sequences published?
\begin{Schunk}
@@ -482,19 +482,19 @@
nature$nelem
\end{Sinput}
\begin{Soutput}
-[1] 1726999
+[1] 1740183
\end{Soutput}
\begin{Sinput}
query("science", "j=science", virtual = T)
science$nelem
\end{Sinput}
\begin{Soutput}
-[1] 1305042
+[1] 1338780
\end{Soutput}
\end{Schunk}
-There are \texttt{1,726,999} sequences published
+There are \texttt{1,740,183} sequences published
in \textit{Nature} and
-\texttt{1,305,042} sequences published in
+\texttt{1,338,780} sequences published in
\textit{Science}, so that the winner is
\textit{Nature}.
@@ -509,10 +509,10 @@
smith$nelem
\end{Sinput}
\begin{Soutput}
-[1] 4164669
+[1] 4183000
\end{Soutput}
\end{Schunk}
-There are \texttt{4,164,669} such sequences.
+There are \texttt{4,183,000} such sequences.
\item[\textbf{YK2.}] How many sequences were published after year 2000 (included)?
\begin{Schunk}
@@ -521,10 +521,10 @@
yk2$nelem
\end{Sinput}
\begin{Soutput}
-[1] 75803186
+[1] 84819267
\end{Soutput}
\end{Schunk}
-There are \texttt{75,803,186} sequences published after year 2000.
+There are \texttt{84,819,267} sequences published after year 2000.
\item[\textbf{Organelle contest.}] Do we have more sequences from chloroplast genomes or from mitochondion genomes?
\begin{Schunk}
@@ -533,19 +533,19 @@
chloro$nelem
\end{Sinput}
\begin{Soutput}
-[1] 174448
+[1] 197367
\end{Soutput}
\begin{Sinput}
query("mito", "o=mitochondrion", virtual = T)
mito$nelem
\end{Sinput}
\begin{Soutput}
-[1] 588090
+[1] 650254
\end{Soutput}
\end{Schunk}
-There are \texttt{174,448} sequences from
+There are \texttt{197,367} sequences from
chloroplast genomes and
-\texttt{588,090} sequences from mitochondrion
+\texttt{650,254} sequences from mitochondrion
genomes, so that the winner is
mitochondrion.
@@ -848,19 +848,20 @@
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}
- \item R version 2.8.0 Under development (unstable) (2008-05-11 r45672), \verb|i386-apple-darwin8.8.2|
- \item Locale: \verb|C|
+ \item R version 2.8.0 (2008-10-20), \verb|i386-apple-darwin8.8.2|
+ \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/C/C|
\item Base packages: base, datasets, grDevices, graphics, methods,
stats, utils
- \item Other packages: MASS~7.2-42, ade4~1.4-7, ape~2.2,
- nlme~3.1-88, seqinr~1.1-6, xtable~1.5-2
+ \item Other packages: MASS~7.2-44, ade4~1.4-9, ape~2.2-2,
+ nlme~3.1-89, quadprog~1.4-11, seqinr~2.0-0, tseries~0.10-16,
+ xtable~1.5-4, zoo~1.5-4
\item Loaded via a namespace (and not attached): grid~2.8.0,
- lattice~0.17-7, tools~2.8.0
+ lattice~0.17-15, tools~2.8.0
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Mon May 12 18:07:53 2008
+ \item \Rlogo{} compilation time was: Sun Oct 26 17:59:06 2008
\item \LaTeX{} compilation time was: \today
\end{itemize}
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