[Seqinr-commits] r1820 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Nov 26 11:34:39 CET 2014
Author: simonpenel
Date: 2014-11-26 11:34:39 +0100 (Wed, 26 Nov 2014)
New Revision: 1820
Modified:
pkg/man/SeqAcnucWeb.Rd
pkg/man/countsubseqs.Rd
pkg/man/getAnnot.Rd
pkg/man/getKeyword.Rd
pkg/man/getLength.Rd
pkg/man/getLocation.Rd
pkg/man/getName.Rd
pkg/man/getSequence.Rd
pkg/man/getTrans.Rd
pkg/man/modifylist.Rd
pkg/man/plot.SeqAcnucWeb.Rd
pkg/man/prepgatannots.Rd
pkg/man/print.SeqAcnucWeb.Rd
pkg/man/print.qaw.Rd
pkg/man/query.Rd
pkg/man/translate.Rd
Log:
Modifications of examples involvng the query function according to
the new features of R-3.1.2 : it is not possible to change an object
belonging the global environment from a package. Eaxmples have been
modified according to a suggestion from Tang Chin Cheung.
Modified: pkg/man/SeqAcnucWeb.Rd
===================================================================
--- pkg/man/SeqAcnucWeb.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/SeqAcnucWeb.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -30,7 +30,7 @@
\examples{
\dontrun{# Need internet connection
choosebank("emblTP")
- query("mylist", "sp=felis catus et t=cds et o=mitochondrion")
+ mylist <- query("mylist", "sp=felis catus et t=cds et o=mitochondrion")
stopifnot(is.SeqAcnucWeb(mylist$req[[1]]))
closebank()
}
Modified: pkg/man/countsubseqs.Rd
===================================================================
--- pkg/man/countsubseqs.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/countsubseqs.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -28,7 +28,7 @@
\examples{
\dontrun{ # Need internet connection
choosebank("emblTP")
- query("mylist", "N=@", virtual = TRUE) # select all (seqs + subseqs)
+ mylist<-query("mylist", "N=@", virtual = TRUE) # select all (seqs + subseqs)
mylist$nelem # 14138094 seqs + subseqs
stopifnot(mylist$nelem == 14138094)
css(glr("mylist")) # 1604500 subsequences only
Modified: pkg/man/getAnnot.Rd
===================================================================
--- pkg/man/getAnnot.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/getAnnot.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -51,7 +51,7 @@
\dontrun{
# Need internet connection
choosebank("emblTP")
- query("fc", "sp=felis catus et t=cds et O=mitochondrion et Y>2001 et no k=partial")
+ fc<-query("fc", "sp=felis catus et t=cds et O=mitochondrion et Y>2001 et no k=partial")
# get the first 5 lines annotating the first sequence:
annots <- getAnnot(fc$req[[1]], nbl = 5)
cat(annots, sep = "\n")
Modified: pkg/man/getKeyword.Rd
===================================================================
--- pkg/man/getKeyword.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/getKeyword.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -43,7 +43,7 @@
\dontrun{
# Need internet connection
choosebank("emblTP")
- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
+ fc<-query("fc", "sp=felis catus et t=cds et o=mitochondrion")
getKeyword(fc$req[[1]])
# Should be:
# [1] "DIVISION ORG" "RELEASE 62" "CYTOCHROME B" "SOURCE" "CDS"
Modified: pkg/man/getLength.Rd
===================================================================
--- pkg/man/getLength.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/getLength.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -50,7 +50,7 @@
\dontrun{
# Need internet connection
choosebank("emblTP")
- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
+ fc <- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
getLength(fc)
closebank()
}
Modified: pkg/man/getLocation.Rd
===================================================================
--- pkg/man/getLocation.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/getLocation.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -46,7 +46,7 @@
\dontrun{
# Need internet connection
choosebank("emblTP")
- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
+ fc <- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
getLocation(fc$req[[5]])
closebank()
}
Modified: pkg/man/getName.Rd
===================================================================
--- pkg/man/getName.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/getName.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -49,7 +49,7 @@
\dontrun{
# Need internet connection
choosebank("emblTP")
- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
+ fc <- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
getName(fc)
closebank()
}
Modified: pkg/man/getSequence.Rd
===================================================================
--- pkg/man/getSequence.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/getSequence.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -50,7 +50,7 @@
#
\dontrun{# Need internet connection
choosebank("emblTP")
- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
+ fc <- query("fc", "sp=felis catus et t=cds et o=mitochondrion")
getSequence(fc$req[[1]])
getSequence(fc$req[[1]], as.string = TRUE)
closebank()
Modified: pkg/man/getTrans.Rd
===================================================================
--- pkg/man/getTrans.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/getTrans.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -111,7 +111,7 @@
# FT complement(152185..153037),138523..138735,138795..138955)
# FT /codon_start=1
choosebank("emblTP")
- query("trans", "N=AE003734.PE35")
+ trans <- query("trans", "N=AE003734.PE35")
getTrans(trans$req[[1]])
}
}
Modified: pkg/man/modifylist.Rd
===================================================================
--- pkg/man/modifylist.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/modifylist.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -58,22 +58,22 @@
\examples{
\dontrun{ # Need internet connection
choosebank("emblTP")
- query("mylist", "sp=felis catus et t=cds", virtual=TRUE)
+ mylist <- query("mylist", "sp=felis catus et t=cds", virtual=TRUE)
mylist$nelem # 603 sequences
stopifnot(mylist$nelem == 603)
# select sequences with at least 1000 bp:
- modifylist("mylist", operation = ">1000", virtual = TRUE)
+ mylist <- modifylist("mylist", operation = ">1000", virtual = TRUE)
mylist$nelem # now, only 132 sequences
stopifnot(mylist$nelem == 132)
# scan for "felis" in annotations:
- modifylist("mylist", op = "felis", type = "scan", virtual = TRUE)
+ mylist <- modifylist("mylist", op = "felis", type = "scan", virtual = TRUE)
mylist$nelem # now, only 33 sequences
stopifnot(mylist$nelem == 33)
# modify by date:
- modifylist("mylist", op = "> 1/jul/2001", type = "date", virtual = TRUE)
+ mylist <- modifylist("mylist", op = "> 1/jul/2001", type = "date", virtual = TRUE)
mylist$nelem # now, only 15 sequences
stopifnot(mylist$nelem == 15)
Modified: pkg/man/plot.SeqAcnucWeb.Rd
===================================================================
--- pkg/man/plot.SeqAcnucWeb.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/plot.SeqAcnucWeb.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -27,9 +27,9 @@
\examples{
\dontrun{
### Need internet connection
- choosebank("hovernucl")
- query("list", "AC=AB000425")
- plot(list$req[[1]])
+ choosebank("hovergendna")
+ mylist <- query("mylist", "AC=AB000425")
+ plot(mylist$req[[1]])
}
}
\keyword{ hplot }
Modified: pkg/man/prepgatannots.Rd
===================================================================
--- pkg/man/prepgatannots.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/prepgatannots.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -66,7 +66,7 @@
choosebank("genbank")
query("mylist","n=AQF16SRRN")
pga() # We want to scan all annotations, including FEATURES
- modifylist("mylist", operation = "strain", type = "scan")
+ mylist <- modifylist("mylist", operation = "strain", type = "scan")
mylist$nelem # should be 1
}
}
Modified: pkg/man/print.SeqAcnucWeb.Rd
===================================================================
--- pkg/man/print.SeqAcnucWeb.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/print.SeqAcnucWeb.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -23,7 +23,7 @@
\dontrun{
### Need internet connection
choosebank("emblTP")
- query("mylist", "sp=felis catus")
+ mylist <- query("mylist", "sp=felis catus")
mylist$req[[1]]
# name length frame ncbicg
# "A06937" "34" "0" "1"
Modified: pkg/man/print.qaw.Rd
===================================================================
--- pkg/man/print.qaw.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/print.qaw.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -23,7 +23,7 @@
\dontrun{
### Need internet connection
choosebank("emblTP")
- query("sp=felis catus")
+ list1 <- query("sp=felis catus")
list1
# 4732 SQ for sp=felis catus
}
Modified: pkg/man/query.Rd
===================================================================
--- pkg/man/query.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/query.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -106,7 +106,7 @@
\dontrun{
# Need internet connection
choosebank("genbank")
- query("bb", "sp=Borrelia burgdorferi")
+ bb <- query("bb", "sp=Borrelia burgdorferi")
# To get the names of the 4 first sequences:
sapply(bb$req[1:4], getName)
# To get the 4 first sequences:
Modified: pkg/man/translate.Rd
===================================================================
--- pkg/man/translate.Rd 2014-11-26 09:12:04 UTC (rev 1819)
+++ pkg/man/translate.Rd 2014-11-26 10:34:39 UTC (rev 1820)
@@ -116,7 +116,7 @@
## FT RSRLKTIGDDLYVTNDVHNHMGDNKRIEAAKAAGMLIHKKLSSLTAADKIQGSWKMDTE
## FT GNPDHLPKM"
choosebank("emblTP")
-query("trans", "N=AE003734.PE35")
+trans <- query("trans", "N=AE003734.PE35")
getTrans(trans$req[[1]])
## Complex transsplicing operations, the correct frame and the correct
## genetic code are automatically used for translation into protein.
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