[BioC] AnnBuilder and Kegg
Paola Pedotti
p.pedotti at lumc.nl
Wed Nov 22 12:22:11 CET 2006
Dear John,
thank you for the suggestions.
However, I downloaded the newest version of AnnBuilder
and still I had the same problem in kegg connection.
******************************************************************************************************************
sessionInfo()
Version 2.3.1 (2006-06-01)
i386-pc-linux-gnu
attached base packages:
[1] "tools" "methods" "stats" "graphics" "grDevices" "utils"
[7] "datasets" "base"
other attached packages:
GO AnnBuilder RSQLite DBI annotate XML
Biobase
"1.12.0" "1.12.0" "0.4-1" "0.1-10" "1.10.0" "0.99-7"
"1.10.0"
mySrcUrls <- c(GO=
"http://www.godatabase.org/dev/database/archive/latest/go_2
00605-termdb.rdf-xml.gz",KEGG="ftp://ftp.genome.ad.jp/pub/kegg/pathways",YG="ftp ://genome-ftp.stanford.edu/pub/yeast/data_download/",HG="ftp://ftp.ncbi.nih.gov/ pub/HomoloGene/old/hmlg.ftp",EG="ftp://ftp.ncbi.nlm.nih.gov/gene/DATA",IPI="ftp: //ftp.ebi.ac.uk/pub/databases/IPI/current/",YEAST="ftp://ftp.yeastgenome.org/pub /yeast/sequence_similarity/domains/",KEGGGENOME="ftp://ftp.genome.ad.jp/pub/kegg /tarfiles/genome",PFAM="ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_releas e/Pfam-A.full.gz")
ppbase<- file.path(.path.package("AnnBuilder"), "data",
"lgtc.ids.1.txt")
myBaseType="gb"
ABPkgBuilder(baseName=ppbase,
+ srcUrls = mySrcUrls,
+ baseMapType = myBaseType,
+ pkgName = "lgtc.221106",
+ pkgPath = '.',
+ organism ="mouse",
+ version ="1.1.0",
+ author = list(author = "Paola Pedotti",
+ maintener ="Paola Pedotti <p.pedotti at lumc.nl>")
+ )
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00010.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00020.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00030.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00031.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00040.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00051.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00052.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00053.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00061.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00062.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00071.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00072.gene
Failed to get data from URL:
ftp://ftp.genome.ad.jp/pub/kegg/pathways//00100.gene
......................
***********************************************************************************************************
Do you have other suggestions?
thanks
Paola
On Tue, 2006-11-21 at 12:13 -0500, John Zhang wrote:
> >
> >Hi everybody,
> >I am trying to annotate my dataset (home spotted array, two colors,
> >mice) using AnnBuilder.
> >Every time I run the program the connection with the kegg
> >website is not working, so I am able to build the annotation
> >package but not for the kegg pathways. Does anybody know how to
> >fix this problem or did anybody find a way to by pass it (like
> >downloading a list of accession numbers and corresponding pathways)?
> >here my script:
>
> I guess the best thing for you to do is to update your R and BioC packages. The
> released version of AnnBuilder is 1.12.0 while you have 1.10.0 on your machine.
>
>
>
> >
> >*******************************************************************************
> **********************
> >
> >library(AnnBuilder)
> >#Loading required package: Biobase
> >#Loading required package: tools
> >#Welcome to Bioconductor
> ># Vignettes contain introductory material. To view,
> ># simply type: openVignette()
> ># For details on reading vignettes, see
> ># the openVignette help page.
> >#Loading required package: annotate
> >
> >library(GO)
> >
> >sessionInfo()
> >
> >#Version 2.3.1 (2006-06-01)
> >#i386-pc-linux-gnu
> >#
> >#attached base packages:
> >#[1] "splines" "tools" "methods" "stats" "graphics"
> >#"grDevices"
> >#[7] "utils" "datasets" "base"
> >#
> >#other attached packages:
> >#
> ># globaltest vsn limma multtest
> ># "4.2.0" "1.10.0" "2.7.3" "1.10.2"
> ># survival affydata affy affyio
> ># "2.20" "1.8.0" "1.10.0" "1.0.0"
> ># KEGG GO AnnBuilder RSQLite
> ># "1.12.0" "1.12.0" "1.10.0" "0.4-1"
> ># DBI annotate XML Biobase
> ># "0.1-10" "1.10.0" "0.99-7" "1.10.0"
> >
> >
> >mySrcUrls <- getSrcUrl("all", organism="Mus Musclusus")
> >
> >base<- file.path(.path.package("AnnBuilder"), "data", "lgtc.ids.1.txt")
> >
> >myBaseType<- "gbNRef"
> >ABPkgBuilder(baseName=base,
> > srcUrls = mySrcUrls,
> > baseMapType = myBaseType,
> > pkgName = "lgtc201106",
> > pkgPath = ".",
> > organism ="Mus Musclusus",
> > version ="1.1.0",
> > author = list(author = "Paola Pedotti",
> > maintener ="Paola Pedotti <p.pedotti at lumc.nl>")
> > )
> >
> >
> >#Failed to get data from URL:
> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07214.gene
> >#Failed to get data from URL:
> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07215.gene
> >#Failed to get data from URL:
> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07216.gene
> >#Failed to get data from URL:
> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07217.gene
> >#Failed to get data from URL:
> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07218.gene
> >#[1] "0 2 2"
> >#Warning message:
> >#cannot open file
> >'/usr/local/lib/R/site-library/AnnBuilder/templates/PKGNAMEGO.1.Rd',
> >reason 'No such file or directory'
> >#The following data sets have been added to the database and will be
> >removed:
> ># [1] "./lgtc161106/data/lgtc161106ACCNUM.rda"
> ># [2] "./lgtc161106/data/lgtc161106CHR.rda"
> ># [3] "./lgtc161106/data/lgtc161106ENZYME.rda"
> ># [4] "./lgtc161106/data/lgtc161106GENENAME.rda"
> ># [5] "./lgtc161106/data/lgtc161106GO.1.rda"
> ># [6] "./lgtc161106/data/lgtc161106GO2ALLPROBES.rda"
> ># [7] "./lgtc161106/data/lgtc161106GO2PROBE.rda"
> ># [8] "./lgtc161106/data/lgtc161106GO.rda"
> ># [9] "./lgtc161106/data/lgtc161106LOCUSID.rda"
> >#[10] "./lgtc161106/data/lgtc161106MAPCOUNTS.rda"
> >#[11] "./lgtc161106/data/lgtc161106MAP.rda"
> >#[12] "./lgtc161106/data/lgtc161106OMIM.rda"
> >#[13] "./lgtc161106/data/lgtc161106ORGANISM.rda"
> >#[14] "./lgtc161106/data/lgtc161106PATH.rda"
> >#[15] "./lgtc161106/data/lgtc161106PMID2PROBE.rda"
> >#[16] "./lgtc161106/data/lgtc161106PMID.rda"
> >#[17] "./lgtc161106/data/lgtc161106QCDATA.rda"
> >#[18] "./lgtc161106/data/lgtc161106QC.rda"
> >#[19] "./lgtc161106/data/lgtc161106REFSEQ.rda"
> >#[20] "./lgtc161106/data/lgtc161106SUMFUNC.rda"
> >#[21] "./lgtc161106/data/lgtc161106SYMBOL.rda"
> >#[22] "./lgtc161106/data/lgtc161106UNIGENE.rda"
> >#Warning message:
> >#Can't
> >copy /usr/local/lib/R/site-library/AnnBuilder/templates/PKGNAMEGO.1.Rd
> >in: copyTemplates(repList, pattern, pkgName, pkgPath)
> >
> >*******************************************************************************
> **********************
> >
> >
> >thank you in advance
> >
> >Paola
> >
> >
> >
> >_______________________________________
> >Center for Human and Clinical Genetics
> >Leiden University Medical Center
> >Postzone: S-04-P, Postbus 9600
> >2300 RC Leiden, The Netherlands
> >Telephone: +31 71 526 9440
> >Fax: +31 71 526 8285
> >
> >_______________________________________________
> >Bioconductor mailing list
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> >https://stat.ethz.ch/mailman/listinfo/bioconductor
> >Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
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