[Seqinr-commits] r1852 - www/src/mainmatter
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 1 16:08:33 CEST 2016
Author: jeanlobry
Date: 2016-06-01 16:08:33 +0200 (Wed, 01 Jun 2016)
New Revision: 1852
Modified:
www/src/mainmatter/querylang.rnw
www/src/mainmatter/querylang.tex
Log:
Now examples run correctly
Modified: www/src/mainmatter/querylang.rnw
===================================================================
--- www/src/mainmatter/querylang.rnw 2016-06-01 12:36:46 UTC (rev 1851)
+++ www/src/mainmatter/querylang.rnw 2016-06-01 14:08:33 UTC (rev 1852)
@@ -28,8 +28,8 @@
<<lowervsupper,fig=F,eval=T>>=
choosebank("emblTP")
-query("lowercase", "sp=escherichia coli", virtual = TRUE)
-query("uppercase", "SP=Escherichia coli", virtual = TRUE)
+lowercase <- query("lowercase", "sp=escherichia coli", virtual = TRUE)
+uppercase <- query("uppercase", "SP=Escherichia coli", virtual = TRUE)
lowercase$nelem == uppercase$nelem
closebank()
@
@@ -41,7 +41,7 @@
<<ambig,fig=F,eval=T>>=
choosebank("emblTP")
-query("ambig","\"sp=Beak and feather disease virus\" AND \"au=ritchie\"", virtual = T)
+ambig <- query("ambig","\"sp=Beak and feather disease virus\" AND \"au=ritchie\"", virtual = T)
ambig$nelem
closebank()
@
@@ -62,9 +62,9 @@
<<borreliaexample,fig=F,eval=T>>=
choosebank("emblTP")
-query("bb","sp=Borrelia burgdorferi",virtual=T)
+bb <- query("bb","sp=Borrelia burgdorferi",virtual=T)
bb$nelem
-query("borrelia","sp=Borrelia",virtual=T)
+borrelia <- query("borrelia","sp=Borrelia",virtual=T)
borrelia$nelem
closebank()
@
@@ -73,9 +73,9 @@
<<sapiens,fig=F,eval=T>>=
choosebank("emblTP")
-query("sapiens","sp=@sapiens@",virtual=T)
+sapiens <- query("sapiens","sp=@sapiens@",virtual=T)
sapiens$nelem
-query("sapienspecies","PS sapiens")
+sapienspecies <- query("sapienspecies","PS sapiens")
getName(sapienspecies)
closebank()
@
@@ -91,9 +91,9 @@
<<tidexample,fig=F,eval=T>>=
choosebank("genbank")
-query("hsn","TID=63221", virtual=T)
+hsn <- query("hsn","TID=63221", virtual=T)
hsn$nelem
-query("hsnsp","PS hsn")
+hsnsp <- query("hsnsp","PS hsn")
getName(hsnsp)
closebank()
@
@@ -105,9 +105,9 @@
characters. Example:
<<exemplekw,fig=F,eval=T>>=
- choosebank("emblTP")
-query("ecoliribprot","sp=escherichia coli AND k=rib@ prot@", virtual=T)
- ecoliribprot$nelem
+choosebank("emblTP")
+ecoliribprot <- query("ecoliribprot","sp=escherichia coli AND k=rib@ prot@", virtual=T)
+ecoliribprot$nelem
closebank()
@
@@ -126,7 +126,7 @@
<<allhscds,fig=F,eval=T>>=
choosebank("emblTP")
-query("hscds","sp=Homo sapiens AND t=cds", virtual=T)
+hscds <- query("hscds","sp=Homo sapiens AND t=cds", virtual=T)
hscds$nelem
closebank()
@
@@ -138,7 +138,7 @@
<<allseqsfromscience,fig=F,eval=T>>=
choosebank("emblTP")
-query("allseqsfromscience","J=Science", virtual=TRUE)
+allseqsfromscience <- query("allseqsfromscience","J=Science", virtual=TRUE)
allseqsfromscience$nelem
closebank()
@
@@ -163,7 +163,7 @@
<<refbibexample,fig=F,eval=T>>=
choosebank("emblTP")
-query("rpro","R=Nature/396/133")
+rpro <- query("rpro","R=Nature/396/133")
getName(rpro)
closebank()
@
@@ -174,7 +174,7 @@
<<authorexample,fig=F,eval=T>>=
choosebank("emblTP")
-query("Graur","AU=Graur")
+Graur <- query("Graur","AU=Graur")
Graur$nelem
closebank()
@
@@ -187,7 +187,7 @@
<<exampleAC,fig=F,eval=T>>=
choosebank("emblTP")
-query("ACexample","AC=AY382159")
+ACexample <- query("ACexample","AC=AY382159")
getName(ACexample$req[[1]])
annotations <- getAnnot(ACexample$req[[1]])
cat(annotations, sep ="\n")
@@ -207,7 +207,7 @@
<<exampleN,fig=F,eval=T>>=
choosebank("emblTP")
-query("Nexample","N=AY382159")
+Nexample <- query("Nexample","N=AY382159")
getName(Nexample$req[[1]])
annotations <- getAnnot(Nexample$req[[1]])
cat(annotations, sep ="\n")
@@ -222,7 +222,7 @@
<<exampleNS,fig=F,eval=T>>=
choosebank("emblTP")
-query("NSexample","NS=@sapiens@")
+NSexample <- query("NSexample","NS=@sapiens@")
NSexample
closebank()
@
@@ -235,7 +235,7 @@
<<exampleNK,fig=F,eval=T>>=
choosebank("emblTP")
-query("NKexample","NK=@sex@")
+NKexample <- query("NKexample","NK=@sex@")
NKexample
closebank()
@
@@ -248,7 +248,7 @@
<<exampleY,fig=F,eval=T>>=
choosebank("emblTP")
-query("Yexample","Y=1999", virtual=TRUE)
+Yexample <- query("Yexample","Y=1999", virtual=TRUE)
Yexample$nelem
closebank()
@
@@ -262,9 +262,9 @@
<<organellescodes,fig=F,eval=T>>=
choosebank("genbank")
- nl <- readfirstrec(type = "SMJ")
- smj <- readsmj(nl = nl, all.add = TRUE)
- smj[!is.na(smj$nature) & smj$nature == "organelle", c("sname","libel")]
+nl <- readfirstrec(type = "SMJ")
+smj <- readsmj(nl = nl, all.add = TRUE)
+smj[!is.na(smj$nature) & smj$nature == "organelle", c("sname","libel")]
closebank()
@
@@ -272,7 +272,7 @@
<<exampleO,fig=F,eval=T>>=
choosebank("emblTP")
-query("Oexample","O=chloroplast", virtual=TRUE)
+Oexample <- query("Oexample","O=chloroplast", virtual=TRUE)
Oexample$nelem
closebank()
@
@@ -286,9 +286,9 @@
<<moleculescodes,fig=F,eval=T>>=
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")]
closebank()
@
@@ -296,7 +296,7 @@
<<exampleM,fig=F,eval=T>>=
choosebank("emblTP")
-query("Mexample","M=DNA", virtual=TRUE)
+Mexample <- query("Mexample","M=DNA", virtual=TRUE)
Mexample$nelem
closebank()
@
@@ -309,14 +309,14 @@
<<emblstatus,fig=F,eval=T>>=
choosebank("embl")
- nl <- readfirstrec(type = "SMJ")
- smj <- readsmj(nl = nl, all.add = TRUE)
- smj[!is.na(smj$nature) & smj$nature == "status", c("sname","libel")]
+nl <- readfirstrec(type = "SMJ")
+smj <- readsmj(nl = nl, all.add = TRUE)
+smj[!is.na(smj$nature) & smj$nature == "status", c("sname","libel")]
closebank()
choosebank("swissprot")
- nl <- readfirstrec(type = "SMJ")
- smj <- readsmj(nl = nl, all.add = TRUE)
- smj[!is.na(smj$nature) & smj$nature == "status", c("sname","libel")]
+nl <- readfirstrec(type = "SMJ")
+smj <- readsmj(nl = nl, all.add = TRUE)
+smj[!is.na(smj$nature) & smj$nature == "status", c("sname","libel")]
closebank()
@
@@ -324,7 +324,7 @@
<<exampleST,fig=F,eval=T>>=
choosebank("swissprot")
-query("STexample","ST=REVIEWED", virtual=TRUE)
+STexample <- query("STexample","ST=REVIEWED", virtual=TRUE)
STexample$nelem
closebank()
@
@@ -340,7 +340,7 @@
choosebank("emblTP")
fileSQ <- system.file("sequences/bb.mne", package = "seqinr")
cat(readLines(fileSQ),sep="\n")
-clfcd("listSQ", file = fileSQ, type = "SQ")
+listSQ <-clfcd("listSQ", file = fileSQ, type = "SQ")
getName(listSQ)
closebank()
@
@@ -357,7 +357,7 @@
choosebank("emblTP")
fileAC <- system.file("sequences/bb.acc", package = "seqinr")
cat(readLines(fileAC),sep="\n")
-clfcd("listAC", file = fileAC, type = "AC")
+listAC <- clfcd("listAC", file = fileAC, type = "AC")
getName(listAC)
closebank()
@
@@ -374,7 +374,7 @@
choosebank("emblTP")
fileKW <- system.file("sequences/bb.kwd", package = "seqinr")
cat(readLines(fileKW),sep="\n")
-clfcd("listKW", file = fileKW, type = "KW")
+listKW <- clfcd("listKW", file = fileKW, type = "KW")
getName(listKW)
closebank()
@
@@ -390,7 +390,7 @@
choosebank("emblTP")
fileSP <- system.file("sequences/bb.sp", package = "seqinr")
cat(readLines(fileSP),sep="\n")
-clfcd("listSP", file = fileSP, type = "SP")
+listSP <- clfcd("listSP", file = fileSP, type = "SP")
getName(listSP)
closebank()
@
@@ -401,11 +401,11 @@
<<examplereuselistname,fig=F,eval=T>>=
choosebank("emblTP")
-query("MyFirstListName", "Y=2000", virtual = TRUE)
+MyFirstListName <- query("MyFirstListName", "Y=2000", virtual = TRUE)
MyFirstListName$nelem
-query("MySecondListName", "SP=Borrelia burgdorferi", virtual = TRUE)
+MySecondListName <- query("MySecondListName", "SP=Borrelia burgdorferi", virtual = TRUE)
MySecondListName$nelem
-query("MyThirdListName", "MyFirstListName AND MySecondListName", virtual = TRUE)
+MyThirdListName <- query("MyThirdListName", "MyFirstListName AND MySecondListName", virtual = TRUE)
MyThirdListName$nelem
closebank()
@
@@ -421,7 +421,7 @@
<<exampleAND,fig=F,eval=T>>=
choosebank("emblTP")
-query("ANDexample","SP=Borrelia burgdorferi AND T=CDS", virtual=TRUE)
+ANDexample <- query("ANDexample","SP=Borrelia burgdorferi AND T=CDS", virtual=TRUE)
ANDexample$nelem
closebank()
@
@@ -436,7 +436,7 @@
<<exampleOR,fig=F,eval=T>>=
choosebank("emblTP")
-query("ORexample","SP=Borrelia burgdorferi OR SP=Escherichia coli", virtual=TRUE)
+ORexample <- query("ORexample","SP=Borrelia burgdorferi OR SP=Escherichia coli", virtual=TRUE)
ORexample$nelem
closebank()
@
@@ -449,7 +449,7 @@
<<exampleOR,fig=F,eval=T>>=
choosebank("emblTP")
-query("NOTexample","SP=Borrelia burgdorferi AND NOT K=PARTIAL", virtual=TRUE)
+NOTexample <- query("NOTexample","SP=Borrelia burgdorferi AND NOT K=PARTIAL", virtual=TRUE)
NOTexample$nelem
closebank()
@
@@ -462,11 +462,11 @@
<<examplePAR,fig=F,eval=T>>=
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)
+A <- query("A","T=TRNA", virtual=TRUE)
+B <- query("B","PAR A", virtual=TRUE)
+C <- query("C","SUB B", virtual=TRUE)
+D <- query("D","PAR C", virtual=TRUE)
+emptySet <- query("emptySet", "B AND NOT D", virtual=TRUE)
emptySet$nelem
closebank()
@
@@ -477,9 +477,9 @@
<<exampleSUB,fig=F,eval=T>>=
choosebank("emblTP")
-query("SUBexample","AC=AE000783",virtual=T)
+SUBexample <- query("SUBexample","AC=AE000783",virtual=T)
SUBexample$nelem
- query("SUBexample2","SUB SUBexample",virtual=T)
+SUBexample2 <- query("SUBexample2","SUB SUBexample",virtual=T)
SUBexample2$nelem
closebank()
@
@@ -491,8 +491,8 @@
<<examplePS,fig=F,eval=T>>=
choosebank("emblTP")
-query("PSexample","K=hyperthermo@",virtual=T)
-query("PSexample2","PS PSexample")
+PSexample <- query("PSexample","K=hyperthermo@",virtual=T)
+PSexample2 <- query("PSexample2","PS PSexample")
getName(PSexample2)
closebank()
@
@@ -504,8 +504,8 @@
<<examplePK,fig=F,eval=T>>=
choosebank("emblTP")
-query("PKexample","AC=AE000783",virtual=T)
-query("PKexample2","PK PKexample")
+PKexample <- query("PKexample","AC=AE000783",virtual=T)
+PKexample2 <- query("PKexample2","PK PKexample")
getName(PKexample2)
closebank()
@
@@ -519,8 +519,8 @@
choosebank("emblTP")
fileSP <- system.file("sequences/bb.sp", package = "seqinr")
cat(readLines(fileSP),sep="\n")
-clfcd("listSP", file = fileSP, type = "SP")
-query("UNexample", "UN listSP", virtual = TRUE)
+listSP <- clfcd("listSP", file = fileSP, type = "SP")
+UNexample <- query("UNexample", "UN listSP", virtual = TRUE)
UNexample$nelem
closebank()
@
@@ -532,10 +532,10 @@
<<exampleSD,fig=F,eval=T>>=
choosebank("emblTP")
-query("hominidae","SP=Hominidae",virtual=T)
-query("hsp","PS hominidae",virtual=T)
+hominidae <- query("hominidae","SP=Hominidae",virtual=T)
+hsp <- query("hsp","PS hominidae",virtual=T)
hsp$nelem
-query("SDexample","SD hsp")
+SDexample <- query("SDexample","SD hsp")
getName(SDexample)
closebank()
@
@@ -547,10 +547,10 @@
<<exampleKD,fig=F,eval=T>>=
choosebank("emblTP")
-query("cat","SP=Felis catus", virtual = TRUE)
-query("catkw","PK cat", virtual = TRUE)
+cat <- query("cat","SP=Felis catus", virtual = TRUE)
+catkw <- query("catkw","PK cat", virtual = TRUE)
catkw$nelem
-query("KDexample","KD catkw", virtual = TRUE)
+KDexample <- query("KDexample","KD catkw", virtual = TRUE)
KDexample$nelem
closebank()
@
Modified: www/src/mainmatter/querylang.tex
===================================================================
--- www/src/mainmatter/querylang.tex 2016-06-01 12:36:46 UTC (rev 1851)
+++ www/src/mainmatter/querylang.tex 2016-06-01 14:08:33 UTC (rev 1852)
@@ -65,8 +65,8 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("lowercase", "sp=escherichia coli", virtual = TRUE)
- query("uppercase", "SP=Escherichia coli", virtual = TRUE)
+ lowercase <- query("lowercase", "sp=escherichia coli", virtual = TRUE)
+ uppercase <- query("uppercase", "SP=Escherichia coli", virtual = TRUE)
lowercase$nelem == uppercase$nelem
\end{Sinput}
\begin{Soutput}
@@ -85,7 +85,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("ambig","\"sp=Beak and feather disease virus\" AND \"au=ritchie\"", virtual = T)
+ ambig <- query("ambig","\"sp=Beak and feather disease virus\" AND \"au=ritchie\"", virtual = T)
ambig$nelem
\end{Sinput}
\begin{Soutput}
@@ -113,14 +113,14 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("bb","sp=Borrelia burgdorferi",virtual=T)
+ bb <- query("bb","sp=Borrelia burgdorferi",virtual=T)
bb$nelem
\end{Sinput}
\begin{Soutput}
[1] 1682
\end{Soutput}
\begin{Sinput}
- query("borrelia","sp=Borrelia",virtual=T)
+ borrelia <- query("borrelia","sp=Borrelia",virtual=T)
borrelia$nelem
\end{Sinput}
\begin{Soutput}
@@ -136,14 +136,14 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("sapiens","sp=@sapiens@",virtual=T)
+ sapiens <- query("sapiens","sp=@sapiens@",virtual=T)
sapiens$nelem
\end{Sinput}
\begin{Soutput}
[1] 2216556
\end{Soutput}
\begin{Sinput}
- query("sapienspecies","PS sapiens")
+ sapienspecies <- query("sapienspecies","PS sapiens")
getName(sapienspecies)
\end{Sinput}
\begin{Soutput}
@@ -191,14 +191,14 @@
\begin{Schunk}
\begin{Sinput}
choosebank("genbank")
- query("hsn","TID=63221", virtual=T)
+ hsn <- query("hsn","TID=63221", virtual=T)
hsn$nelem
\end{Sinput}
\begin{Soutput}
-[1] 1355
+[1] 1358
\end{Soutput}
\begin{Sinput}
- query("hsnsp","PS hsn")
+ hsnsp <- query("hsnsp","PS hsn")
getName(hsnsp)
\end{Sinput}
\begin{Soutput}
@@ -217,9 +217,9 @@
\begin{Schunk}
\begin{Sinput}
- choosebank("emblTP")
- query("ecoliribprot","sp=escherichia coli AND k=rib@ prot@", virtual=T)
- ecoliribprot$nelem
+ choosebank("emblTP")
+ ecoliribprot <- query("ecoliribprot","sp=escherichia coli AND k=rib@ prot@", virtual=T)
+ ecoliribprot$nelem
\end{Sinput}
\begin{Soutput}
[1] 105
@@ -259,7 +259,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("hscds","sp=Homo sapiens AND t=cds", virtual=T)
+ hscds <- query("hscds","sp=Homo sapiens AND t=cds", virtual=T)
hscds$nelem
\end{Sinput}
\begin{Soutput}
@@ -278,7 +278,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("allseqsfromscience","J=Science", virtual=TRUE)
+ allseqsfromscience <- query("allseqsfromscience","J=Science", virtual=TRUE)
allseqsfromscience$nelem
\end{Sinput}
\begin{Soutput}
@@ -323,7 +323,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("rpro","R=Nature/396/133")
+ rpro <- query("rpro","R=Nature/396/133")
getName(rpro)
\end{Sinput}
\begin{Soutput}
@@ -341,7 +341,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("Graur","AU=Graur")
+ Graur <- query("Graur","AU=Graur")
Graur$nelem
\end{Sinput}
\begin{Soutput}
@@ -361,7 +361,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("ACexample","AC=AY382159")
+ ACexample <- query("ACexample","AC=AY382159")
getName(ACexample$req[[1]])
\end{Sinput}
\begin{Soutput}
@@ -435,7 +435,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("Nexample","N=AY382159")
+ Nexample <- query("Nexample","N=AY382159")
getName(Nexample$req[[1]])
\end{Sinput}
\begin{Soutput}
@@ -504,7 +504,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("NSexample","NS=@sapiens@")
+ NSexample <- query("NSexample","NS=@sapiens@")
NSexample
\end{Sinput}
\begin{Soutput}
@@ -524,7 +524,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("NKexample","NK=@sex@")
+ NKexample <- query("NKexample","NK=@sex@")
NKexample
\end{Sinput}
\begin{Soutput}
@@ -544,7 +544,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("Yexample","Y=1999", virtual=TRUE)
+ Yexample <- query("Yexample","Y=1999", virtual=TRUE)
Yexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -565,18 +565,18 @@
\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
-5278 CHLOROPLAST Chloroplast genome
-5279 CHROMATOPHORE <NA>
-5280 HYDROGENOSOME <NA>
-5281 MITOCHONDRION Mitochondrial genome
-5282 NUCLEOMORPH Nucleomorph genome
-5283 PLASTID non-green plastid genome
+5914 CHLOROPLAST Chloroplast genome
+5915 CHROMATOPHORE <NA>
+5916 HYDROGENOSOME <NA>
+5917 MITOCHONDRION Mitochondrial genome
+5918 NUCLEOMORPH Nucleomorph genome
+5919 PLASTID non-green plastid genome
\end{Soutput}
\begin{Sinput}
closebank()
@@ -588,7 +588,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("Oexample","O=chloroplast", virtual=TRUE)
+ Oexample <- query("Oexample","O=chloroplast", virtual=TRUE)
Oexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -609,9 +609,9 @@
\begin{Schunk}
\begin{Sinput}
choosebank("genbank")
- nl <- readfirstrec(type = "SMJ")
- smj <- readsmj(nl = nl, all.add = TRUE)
- smj[!is.na(smj$nature) & smj$nature == "molecule", c("sname","libel")]
+ nl <- readfirstrec(type = "SMJ")
+ smj <- readsmj(nl = nl, all.add = TRUE)
+ smj[!is.na(smj$nature) & smj$nature == "molecule", c("sname","libel")]
\end{Sinput}
\begin{Soutput}
sname libel
@@ -632,7 +632,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("Mexample","M=DNA", virtual=TRUE)
+ Mexample <- query("Mexample","M=DNA", virtual=TRUE)
Mexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -652,9 +652,9 @@
\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
@@ -672,9 +672,9 @@
\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
@@ -691,11 +691,11 @@
\begin{Schunk}
\begin{Sinput}
choosebank("swissprot")
- query("STexample","ST=REVIEWED", virtual=TRUE)
+ STexample <- query("STexample","ST=REVIEWED", virtual=TRUE)
STexample$nelem
\end{Sinput}
\begin{Soutput}
-[1] 545388
+[1] 549008
\end{Soutput}
\begin{Sinput}
closebank()
@@ -738,7 +738,7 @@
AB041949.VLSE
\end{Soutput}
\begin{Sinput}
- clfcd("listSQ", file = fileSQ, type = "SQ")
+ listSQ <-clfcd("listSQ", file = fileSQ, type = "SQ")
getName(listSQ)
\end{Sinput}
\begin{Soutput}
@@ -790,7 +790,7 @@
AY500383
\end{Soutput}
\begin{Sinput}
- clfcd("listAC", file = fileAC, type = "AC")
+ listAC <- clfcd("listAC", file = fileAC, type = "AC")
getName(listAC)
\end{Sinput}
\begin{Soutput}
@@ -841,7 +841,7 @@
PROMOTER REGION
\end{Soutput}
\begin{Sinput}
- clfcd("listKW", file = fileKW, type = "KW")
+ listKW <- clfcd("listKW", file = fileKW, type = "KW")
getName(listKW)
\end{Sinput}
\begin{Soutput}
@@ -892,7 +892,7 @@
BORRELIA JAPONICA
\end{Soutput}
\begin{Sinput}
- clfcd("listSP", file = fileSP, type = "SP")
+ listSP <- clfcd("listSP", file = fileSP, type = "SP")
getName(listSP)
\end{Sinput}
\begin{Soutput}
@@ -916,21 +916,21 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("MyFirstListName", "Y=2000", virtual = TRUE)
+ MyFirstListName <- query("MyFirstListName", "Y=2000", virtual = TRUE)
MyFirstListName$nelem
\end{Sinput}
\begin{Soutput}
[1] 885225
\end{Soutput}
\begin{Sinput}
- query("MySecondListName", "SP=Borrelia burgdorferi", virtual = TRUE)
+ MySecondListName <- query("MySecondListName", "SP=Borrelia burgdorferi", virtual = TRUE)
MySecondListName$nelem
\end{Sinput}
\begin{Soutput}
[1] 1682
\end{Soutput}
\begin{Sinput}
- query("MyThirdListName", "MyFirstListName AND MySecondListName", virtual = TRUE)
+ MyThirdListName <- query("MyThirdListName", "MyFirstListName AND MySecondListName", virtual = TRUE)
MyThirdListName$nelem
\end{Sinput}
\begin{Soutput}
@@ -953,7 +953,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("ANDexample","SP=Borrelia burgdorferi AND T=CDS", virtual=TRUE)
+ ANDexample <- query("ANDexample","SP=Borrelia burgdorferi AND T=CDS", virtual=TRUE)
ANDexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -975,7 +975,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("ORexample","SP=Borrelia burgdorferi OR SP=Escherichia coli", virtual=TRUE)
+ ORexample <- query("ORexample","SP=Borrelia burgdorferi OR SP=Escherichia coli", virtual=TRUE)
ORexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -995,7 +995,7 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("NOTexample","SP=Borrelia burgdorferi AND NOT K=PARTIAL", virtual=TRUE)
+ NOTexample <- query("NOTexample","SP=Borrelia burgdorferi AND NOT K=PARTIAL", virtual=TRUE)
NOTexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -1015,11 +1015,11 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("A","T=TRNA", virtual=TRUE)
- query("B","PAR A", virtual=TRUE)
- query("C","SUB B", virtual=TRUE)
- query("D","PAR C", virtual=TRUE)
- query("emptySet", "B AND NOT D", virtual=TRUE)
+ A <- query("A","T=TRNA", virtual=TRUE)
+ B <- query("B","PAR A", virtual=TRUE)
+ C <- query("C","SUB B", virtual=TRUE)
+ D <- query("D","PAR C", virtual=TRUE)
+ emptySet <- query("emptySet", "B AND NOT D", virtual=TRUE)
emptySet$nelem
\end{Sinput}
\begin{Soutput}
@@ -1037,14 +1037,14 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("SUBexample","AC=AE000783",virtual=T)
+ SUBexample <- query("SUBexample","AC=AE000783",virtual=T)
SUBexample$nelem
\end{Sinput}
\begin{Soutput}
[1] 70
\end{Soutput}
\begin{Sinput}
- query("SUBexample2","SUB SUBexample",virtual=T)
+ SUBexample2 <- query("SUBexample2","SUB SUBexample",virtual=T)
SUBexample2$nelem
\end{Sinput}
\begin{Soutput}
@@ -1063,8 +1063,8 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("PSexample","K=hyperthermo@",virtual=T)
- query("PSexample2","PS PSexample")
+ PSexample <- query("PSexample","K=hyperthermo@",virtual=T)
+ PSexample2 <- query("PSexample2","PS PSexample")
getName(PSexample2)
\end{Sinput}
\begin{Soutput}
@@ -1084,8 +1084,8 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("PKexample","AC=AE000783",virtual=T)
- query("PKexample2","PK PKexample")
+ PKexample <- query("PKexample","AC=AE000783",virtual=T)
+ PKexample2 <- query("PKexample2","PK PKexample")
getName(PKexample2)
\end{Sinput}
\begin{Soutput}
@@ -1131,8 +1131,8 @@
BORRELIA JAPONICA
\end{Soutput}
\begin{Sinput}
- clfcd("listSP", file = fileSP, type = "SP")
- query("UNexample", "UN listSP", virtual = TRUE)
+ listSP <- clfcd("listSP", file = fileSP, type = "SP")
+ UNexample <- query("UNexample", "UN listSP", virtual = TRUE)
UNexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -1151,15 +1151,15 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("hominidae","SP=Hominidae",virtual=T)
- query("hsp","PS hominidae",virtual=T)
+ hominidae <- query("hominidae","SP=Hominidae",virtual=T)
+ hsp <- query("hsp","PS hominidae",virtual=T)
hsp$nelem
\end{Sinput}
\begin{Soutput}
[1] 19
\end{Soutput}
\begin{Sinput}
- query("SDexample","SD hsp")
+ SDexample <- query("SDexample","SD hsp")
getName(SDexample)
\end{Sinput}
\begin{Soutput}
@@ -1189,15 +1189,15 @@
\begin{Schunk}
\begin{Sinput}
choosebank("emblTP")
- query("cat","SP=Felis catus", virtual = TRUE)
- query("catkw","PK cat", virtual = TRUE)
+ cat <- query("cat","SP=Felis catus", virtual = TRUE)
+ catkw <- query("catkw","PK cat", virtual = TRUE)
catkw$nelem
\end{Sinput}
\begin{Soutput}
[1] 540
\end{Soutput}
\begin{Sinput}
- query("KDexample","KD catkw", virtual = TRUE)
+ KDexample <- query("KDexample","KD catkw", virtual = TRUE)
KDexample$nelem
\end{Sinput}
\begin{Soutput}
@@ -1216,20 +1216,20 @@
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: Wed Jun 11 10:58:16 2014
+ \item \Rlogo{} compilation time was: Wed Jun 1 16:07:13 2016
\item \LaTeX{} compilation time was: \today
\end{itemize}
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