Candida albicans AnnotationData Package
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@guest-user-4897
Last seen 7.1 years ago
Dear Annotation Data Package developers, I was wondering if anyone is willing to develop Annotation Data Package for Candida albicans which will be very much helpful for many researchers in different labs. The whole genome is already available (cgd) and can be used easily. Thank you very much, Baharul -- output of sessionInfo(): Bioconductor Annotation Data Package for Candida albicans. -- Sent via the guest posting facility at bioconductor.org.
Annotation Annotation • 488 views
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@james-w-macdonald-5106
Last seen 17 hours ago
United States
Hi Baharul, You can do it yourself using AnnotationForge and the makeOrgPackageFromNCBI function. Note that the tax_id for C. albicans is 5476. Best, Jim On 2/24/2014 12:22 PM, Baharul [guest] wrote: > Dear Annotation Data Package developers, > I was wondering if anyone is willing to develop Annotation Data Package for Candida albicans which will be very much helpful for many researchers in different labs. The whole genome is already available (cgd) and can be used easily. > Thank you very much, > Baharul > > -- output of sessionInfo(): > > Bioconductor Annotation Data Package for Candida albicans. > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi, I just run a code inherited from a recent nature paper: https://github.com/RoundLab/Ost_CandidaRNASeq However, I got a lot of errors with annotation forge. Would you please help me? Yesterday, I had another error. Today I have rerun it, and I got another error. :( Thank you very much for your help!

Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version


 library("biomaRt")
    library("GenomeInfoDb")
    library(AnnotationDbi)
    library(Biobase)
    library(AnnotationForge)
    library("GO.db")


    path1<-tcltk::tk_choose.dir(getwd(), "Choose the folder for Analysis")
    # A window will popup and ask you to select the folder containg the data  
    setwd(path1)
    path1

    makeOrgPackageFromNCBI(version = "0.1", 
                           author = "Trinh Phan-Canh <phan@univie.ac.at>", 
                           maintainer = "Trinh Phan-Canh <phan@univie.ac.at>", 
                           outputDir = "data", 
                           tax_id = "237561", genus = "Candida", species =  "albicans")


If files are not cached locally this may take awhile to assemble a 12 GB cache databse in the NCBIFilesDir directory. Subsequent calls to this function should be faster (seconds). The cache will try to rebuild once per day.
preparing data from NCBI ...
starting download for 
[1] gene2pubmed.gz
[2] gene2accession.gz
[3] gene2refseq.gz
[4] gene_info.gz
[5] gene2go.gz
getting data for gene2pubmed.gz
extracting data for our organism from : gene2pubmed
getting data for gene2accession.gz
extracting data for our organism from : gene2accession
getting data for gene2refseq.gz
extracting data for our organism from : gene2refseq
getting data for gene_info.gz
extracting data for our organism from : gene_info
getting data for gene2go.gz
extracting data for our organism from : gene2go
processing gene2pubmed
processing gene_info: chromosomes
processing gene_info: description
processing alias data
processing refseq data
processing accession data
processing GO data
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
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