[Seqinr-commits] r1803 - www/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jun 6 21:41:26 CEST 2014
Author: jeanlobry
Date: 2014-06-06 21:41:26 +0200 (Fri, 06 Jun 2014)
New Revision: 1803
Modified:
www/src/mainmatter/querylang.rnw
www/src/mainmatter/querylang.tex
Log:
compil 3.0-11
Modified: www/src/mainmatter/querylang.rnw
===================================================================
--- www/src/mainmatter/querylang.rnw 2014-06-06 19:29:31 UTC (rev 1802)
+++ www/src/mainmatter/querylang.rnw 2014-06-06 19:41:26 UTC (rev 1803)
@@ -6,6 +6,7 @@
\author{Lobry, J.R.}
\begin{document}
+\SweaveOpts{concordance=TRUE}
\SweaveInput{../config/commonrnw.rnw}
\maketitle
\tableofcontents
Modified: www/src/mainmatter/querylang.tex
===================================================================
--- www/src/mainmatter/querylang.tex 2014-06-06 19:29:31 UTC (rev 1802)
+++ www/src/mainmatter/querylang.tex 2014-06-06 19:41:26 UTC (rev 1803)
@@ -7,6 +7,7 @@
\usepackage{Sweave}
\begin{document}
+\input{querylang-concordance}
%
% To change the R input/output style:
%
@@ -84,8 +85,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("ambig", "\"sp=Beak and feather disease virus\" AND \"au=ritchie\"",
- virtual = T)
+ query("ambig","\"sp=Beak and feather disease virus\" AND \"au=ritchie\"", virtual = T)
ambig$nelem
\end{Sinput}
\begin{Soutput}
@@ -113,14 +113,14 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("bb", "sp=Borrelia burgdorferi", virtual = T)
+ query("bb","sp=Borrelia burgdorferi",virtual=T)
bb$nelem
\end{Sinput}
\begin{Soutput}
[1] 1682
\end{Soutput}
\begin{Sinput}
- query("borrelia", "sp=Borrelia", virtual = T)
+ query("borrelia","sp=Borrelia",virtual=T)
borrelia$nelem
\end{Sinput}
\begin{Soutput}
@@ -136,14 +136,14 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("sapiens", "sp=@sapiens@", virtual = T)
+ query("sapiens","sp=@sapiens@",virtual=T)
sapiens$nelem
\end{Sinput}
\begin{Soutput}
[1] 2216556
\end{Soutput}
\begin{Sinput}
- query("sapienspecies", "PS sapiens")
+ query("sapienspecies","PS sapiens")
getName(sapienspecies)
\end{Sinput}
\begin{Soutput}
@@ -191,14 +191,14 @@
\begin{Schunk}
\begin{Sinput}
choosebank("genbank")
- query("hsn", "TID=63221", virtual = T)
+ query("hsn","TID=63221", virtual=T)
hsn$nelem
\end{Sinput}
\begin{Soutput}
-[1] 1346
+[1] 1355
\end{Soutput}
\begin{Sinput}
- query("hsnsp", "PS hsn")
+ query("hsnsp","PS hsn")
getName(hsnsp)
\end{Sinput}
\begin{Soutput}
@@ -217,10 +217,9 @@
\begin{Schunk}
\begin{Sinput}
- choosebank("emblTP")
- query("ecoliribprot", "sp=escherichia coli AND k=rib@ prot@",
- virtual = T)
- ecoliribprot$nelem
+ choosebank("emblTP")
+ query("ecoliribprot","sp=escherichia coli AND k=rib@ prot@", virtual=T)
+ ecoliribprot$nelem
\end{Sinput}
\begin{Soutput}
[1] 105
@@ -260,7 +259,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("hscds", "sp=Homo sapiens AND t=cds", virtual = T)
+ query("hscds","sp=Homo sapiens AND t=cds", virtual=T)
hscds$nelem
\end{Sinput}
\begin{Soutput}
@@ -279,7 +278,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("allseqsfromscience", "J=Science", virtual = TRUE)
+ query("allseqsfromscience","J=Science", virtual=TRUE)
allseqsfromscience$nelem
\end{Sinput}
\begin{Soutput}
@@ -298,8 +297,7 @@
choosebank("emblTP")
nl <- readfirstrec(type = "SMJ")
smj <- readsmj(nl = nl, all.add = TRUE)
- head(smj[!is.na(smj$nature) & smj$nature == "journal", c("sname",
- "libel")])
+ head(smj[!is.na(smj$nature) & smj$nature == "journal", c("sname","libel")])
\end{Sinput}
\begin{Soutput}
sname libel
@@ -325,7 +323,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("rpro", "R=Nature/396/133")
+ query("rpro","R=Nature/396/133")
getName(rpro)
\end{Sinput}
\begin{Soutput}
@@ -343,7 +341,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("Graur", "AU=Graur")
+ query("Graur","AU=Graur")
Graur$nelem
\end{Sinput}
\begin{Soutput}
@@ -363,7 +361,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("ACexample", "AC=AY382159")
+ query("ACexample","AC=AY382159")
getName(ACexample$req[[1]])
\end{Sinput}
\begin{Soutput}
@@ -371,7 +369,7 @@
\end{Soutput}
\begin{Sinput}
annotations <- getAnnot(ACexample$req[[1]])
- cat(annotations, sep = "\n")
+ cat(annotations, sep ="\n")
\end{Sinput}
\begin{Soutput}
ID AY382159 standard; genomic DNA; PRO; 783 BP.
@@ -437,7 +435,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("Nexample", "N=AY382159")
+ query("Nexample","N=AY382159")
getName(Nexample$req[[1]])
\end{Sinput}
\begin{Soutput}
@@ -445,7 +443,7 @@
\end{Soutput}
\begin{Sinput}
annotations <- getAnnot(Nexample$req[[1]])
- cat(annotations, sep = "\n")
+ cat(annotations, sep ="\n")
\end{Sinput}
\begin{Soutput}
ID AY382159 standard; genomic DNA; PRO; 783 BP.
@@ -506,7 +504,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("Yexample", "Y=1999", virtual = TRUE)
+ query("Yexample","Y=1999", virtual=TRUE)
Yexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -527,17 +525,18 @@
\begin{Schunk}
\begin{Sinput}
choosebank("genbank")
- nl <- readfirstrec(type = "SMJ")
- smj <- readsmj(nl = nl, all.add = TRUE)
- smj[!is.na(smj$nature) & smj$nature == "organelle", c("sname",
- "libel")]
+ nl <- readfirstrec(type = "SMJ")
+ smj <- readsmj(nl = nl, all.add = TRUE)
+ smj[!is.na(smj$nature) & smj$nature == "organelle", c("sname","libel")]
\end{Sinput}
\begin{Soutput}
sname libel
-4078 CHLOROPLAST Chloroplast genome
-4079 MITOCHONDRION Mitochondrial genome
-4080 NUCLEOMORPH Nucleomorph genome
-4081 PLASTID non-green plastid genome
+5278 CHLOROPLAST Chloroplast genome
+5279 CHROMATOPHORE <NA>
+5280 HYDROGENOSOME <NA>
+5281 MITOCHONDRION Mitochondrial genome
+5282 NUCLEOMORPH Nucleomorph genome
+5283 PLASTID non-green plastid genome
\end{Soutput}
\begin{Sinput}
closebank()
@@ -549,7 +548,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("Oexample", "O=chloroplast", virtual = TRUE)
+ query("Oexample","O=chloroplast", virtual=TRUE)
Oexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -570,22 +569,18 @@
\begin{Schunk}
\begin{Sinput}
choosebank("genbank")
- nl <- readfirstrec(type = "SMJ")
- smj <- readsmj(nl = nl, all.add = TRUE)
- smj[!is.na(smj$nature) & smj$nature == "molecule", c("sname",
- "libel")]
+ nl <- readfirstrec(type = "SMJ")
+ smj <- readsmj(nl = nl, all.add = TRUE)
+ smj[!is.na(smj$nature) & smj$nature == "molecule", c("sname","libel")]
\end{Sinput}
\begin{Soutput}
- sname libel
-4 CRNA <NA>
-5 DNA Sequenced molecule is DNA
-6 MRNA sequenced molecule is mRNA
-7 RNA Sequenced molecule is RNA
-8 RRNA sequenced molecule is rRNA
-9 SCRNA sequenced molecule is small cytoplasmic RNA
-10 SNORNA sequenced molecule is small nucleolar RNA
-11 SNRNA sequenced molecule is small nuclear RNA
-12 TRNA sequenced molecule is tRNA
+ sname libel
+4 CRNA Sequenced molecule is complementary RNA
+5 DNA Sequenced molecule is DNA
+6 MRNA sequenced molecule is mRNA
+7 RNA Sequenced molecule is RNA
+8 RRNA sequenced molecule is rRNA
+9 TRNA sequenced molecule is tRNA
\end{Soutput}
\begin{Sinput}
closebank()
@@ -597,7 +592,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("Mexample", "M=DNA", virtual = TRUE)
+ query("Mexample","M=DNA", virtual=TRUE)
Mexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -617,10 +612,9 @@
\begin{Schunk}
\begin{Sinput}
choosebank("embl")
- nl <- readfirstrec(type = "SMJ")
- smj <- readsmj(nl = nl, all.add = TRUE)
- smj[!is.na(smj$nature) & smj$nature == "status", c("sname",
- "libel")]
+ nl <- readfirstrec(type = "SMJ")
+ smj <- readsmj(nl = nl, all.add = TRUE)
+ smj[!is.na(smj$nature) & smj$nature == "status", c("sname","libel")]
\end{Sinput}
\begin{Soutput}
sname libel
@@ -638,10 +632,9 @@
\begin{Sinput}
closebank()
choosebank("swissprot")
- nl <- readfirstrec(type = "SMJ")
- smj <- readsmj(nl = nl, all.add = TRUE)
- smj[!is.na(smj$nature) & smj$nature == "status", c("sname",
- "libel")]
+ nl <- readfirstrec(type = "SMJ")
+ smj <- readsmj(nl = nl, all.add = TRUE)
+ smj[!is.na(smj$nature) & smj$nature == "status", c("sname","libel")]
\end{Sinput}
\begin{Soutput}
sname libel
@@ -658,11 +651,11 @@
\begin{Schunk}
\begin{Sinput}
choosebank("swissprot")
- query("STexample", "ST=REVIEWED", virtual = TRUE)
+ query("STexample","ST=REVIEWED", virtual=TRUE)
STexample$nelem
\end{Sinput}
\begin{Soutput}
-[1] 509019
+[1] 545388
\end{Soutput}
\begin{Sinput}
closebank()
@@ -680,7 +673,7 @@
\begin{Sinput}
choosebank("emblTP")
fileSQ <- system.file("sequences/bb.mne", package = "seqinr")
- cat(readLines(fileSQ), sep = "\n")
+ cat(readLines(fileSQ),sep="\n")
\end{Sinput}
\begin{Soutput}
A04009.OSPA
@@ -732,7 +725,7 @@
\begin{Sinput}
choosebank("emblTP")
fileAC <- system.file("sequences/bb.acc", package = "seqinr")
- cat(readLines(fileAC), sep = "\n")
+ cat(readLines(fileAC),sep="\n")
\end{Sinput}
\begin{Soutput}
AY382159
@@ -783,7 +776,7 @@
\begin{Sinput}
choosebank("emblTP")
fileKW <- system.file("sequences/bb.kwd", package = "seqinr")
- cat(readLines(fileKW), sep = "\n")
+ cat(readLines(fileKW),sep="\n")
\end{Sinput}
\begin{Soutput}
PLASMID
@@ -809,7 +802,7 @@
\end{Soutput}
\begin{Sinput}
clfcd("listKW", file = fileKW, type = "KW")
- getName(listKW)
+ getName(listKW)
\end{Sinput}
\begin{Soutput}
[1] "PLASMID" "CIRCULAR" "PARTIAL" "5'-PARTIAL"
@@ -834,7 +827,7 @@
\begin{Sinput}
choosebank("emblTP")
fileSP <- system.file("sequences/bb.sp", package = "seqinr")
- cat(readLines(fileSP), sep = "\n")
+ cat(readLines(fileSP),sep="\n")
\end{Sinput}
\begin{Soutput}
BORRELIA ANSERINA
@@ -860,7 +853,7 @@
\end{Soutput}
\begin{Sinput}
clfcd("listSP", file = fileSP, type = "SP")
- getName(listSP)
+ getName(listSP)
\end{Sinput}
\begin{Soutput}
[1] "BORRELIA ANSERINA" "BORRELIA CORIACEAE" "BORRELIA PARKERI"
@@ -897,8 +890,7 @@
[1] 1682
\end{Soutput}
\begin{Sinput}
- query("MyThirdListName", "MyFirstListName AND MySecondListName",
- virtual = TRUE)
+ query("MyThirdListName", "MyFirstListName AND MySecondListName", virtual = TRUE)
MyThirdListName$nelem
\end{Sinput}
\begin{Soutput}
@@ -921,7 +913,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("ANDexample", "SP=Borrelia burgdorferi AND T=CDS", virtual = TRUE)
+ query("ANDexample","SP=Borrelia burgdorferi AND T=CDS", virtual=TRUE)
ANDexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -943,8 +935,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("ORexample", "SP=Borrelia burgdorferi OR SP=Escherichia coli",
- virtual = TRUE)
+ query("ORexample","SP=Borrelia burgdorferi OR SP=Escherichia coli", virtual=TRUE)
ORexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -964,8 +955,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("NOTexample", "SP=Borrelia burgdorferi AND NOT K=PARTIAL",
- virtual = TRUE)
+ query("NOTexample","SP=Borrelia burgdorferi AND NOT K=PARTIAL", virtual=TRUE)
NOTexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -985,11 +975,11 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("A", "T=TRNA", virtual = TRUE)
- query("B", "PAR A", virtual = TRUE)
- query("C", "SUB B", virtual = TRUE)
- query("D", "PAR C", virtual = TRUE)
- query("emptySet", "B AND NOT D", virtual = TRUE)
+ query("A","T=TRNA", virtual=TRUE)
+ query("B","PAR A", virtual=TRUE)
+ query("C","SUB B", virtual=TRUE)
+ query("D","PAR C", virtual=TRUE)
+ query("emptySet", "B AND NOT D", virtual=TRUE)
emptySet$nelem
\end{Sinput}
\begin{Soutput}
@@ -1007,14 +997,14 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("SUBexample", "AC=AE000783", virtual = T)
+ query("SUBexample","AC=AE000783",virtual=T)
SUBexample$nelem
\end{Sinput}
\begin{Soutput}
[1] 70
\end{Soutput}
\begin{Sinput}
- query("SUBexample2", "SUB SUBexample", virtual = T)
+ query("SUBexample2","SUB SUBexample",virtual=T)
SUBexample2$nelem
\end{Sinput}
\begin{Soutput}
@@ -1033,8 +1023,8 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("PSexample", "K=hyperthermo@", virtual = T)
- query("PSexample2", "PS PSexample")
+ query("PSexample","K=hyperthermo@",virtual=T)
+ query("PSexample2","PS PSexample")
getName(PSexample2)
\end{Sinput}
\begin{Soutput}
@@ -1054,8 +1044,8 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("PKexample", "AC=AE000783", virtual = T)
- query("PKexample2", "PK PKexample")
+ query("PKexample","AC=AE000783",virtual=T)
+ query("PKexample2","PK PKexample")
getName(PKexample2)
\end{Sinput}
\begin{Soutput}
@@ -1076,7 +1066,7 @@
\begin{Sinput}
choosebank("emblTP")
fileSP <- system.file("sequences/bb.sp", package = "seqinr")
- cat(readLines(fileSP), sep = "\n")
+ cat(readLines(fileSP),sep="\n")
\end{Sinput}
\begin{Soutput}
BORRELIA ANSERINA
@@ -1103,10 +1093,10 @@
\begin{Sinput}
clfcd("listSP", file = fileSP, type = "SP")
query("UNexample", "UN listSP", virtual = TRUE)
- UNexample$nelem
+ UNexample$nelem
\end{Sinput}
\begin{Soutput}
-[1] 2786
+[1] 2877
\end{Soutput}
\begin{Sinput}
closebank()
@@ -1121,16 +1111,16 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("hominidae", "SP=Hominidae", virtual = T)
- query("hsp", "PS hominidae", virtual = T)
+ query("hominidae","SP=Hominidae",virtual=T)
+ query("hsp","PS hominidae",virtual=T)
hsp$nelem
\end{Sinput}
\begin{Soutput}
[1] 19
\end{Soutput}
\begin{Sinput}
- query("SDexample", "SD hsp")
- getName(SDexample)
+ query("SDexample","SD hsp")
+ getName(SDexample)
\end{Sinput}
\begin{Soutput}
[1] "HOMINIDAE" "PONGO"
@@ -1159,15 +1149,15 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("cat", "SP=Felis catus", virtual = TRUE)
- query("catkw", "PK cat", virtual = TRUE)
+ query("cat","SP=Felis catus", virtual = TRUE)
+ query("catkw","PK cat", virtual = TRUE)
catkw$nelem
\end{Sinput}
\begin{Soutput}
[1] 540
\end{Soutput}
\begin{Sinput}
- query("KDexample", "KD catkw", virtual = TRUE)
+ query("KDexample","KD catkw", virtual = TRUE)
KDexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -1186,20 +1176,20 @@
This part was compiled under the following \Rlogo{}~environment:
\begin{itemize}\raggedright
- \item R version 2.10.0 (2009-10-26), \verb|i386-apple-darwin8.11.1|
- \item Locale: \verb|fr_FR.UTF-8/fr_FR.UTF-8/fr_FR.UTF-8/C/C/C|
+ \item R version 3.1.0 (2014-04-10), \verb|x86_64-apple-darwin13.1.0|
+ \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: ade4~1.4-13, ape~2.4, grImport~0.4-4,
- MASS~7.3-3, quadprog~1.4-11, seqinr~2.0-7, tseries~0.10-21,
- XML~2.6-0, xtable~1.5-5, zoo~1.5-8
- \item Loaded via a namespace (and not attached): gee~4.13-14,
- lattice~0.17-26, nlme~3.1-96, tools~2.10.0
+ \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
\end{itemize}
There were two compilation steps:
\begin{itemize}
- \item \Rlogo{} compilation time was: Thu Nov 5 13:21:38 2009
+ \item \Rlogo{} compilation time was: Fri Jun 6 21:34:45 2014
\item \LaTeX{} compilation time was: \today
\end{itemize}
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