[BioC] missing AnnBuilder parser

John Zhang jzhang at jimmy.harvard.edu
Mon Apr 11 20:49:20 CEST 2005

>I'm trying to rebuild my annotation package for an Agilent chip using
>Resourcerer and it's not finder one of the parsers.
>The basic error is:
>>resourcerer2BioC("Agilent_HumanGenome.zip", organism="human")

I have checked in the bug fixes. Please look for a new build (1.1.1) of 
Resourcerer in the next few days. Meanwhile, you may try to fix the bug yourself 
by changing the argument baseMapType = c("gb", "ug", "ll") to baseMapType = 
c("gbNRef", "gb", "ug") of resourcerer2BioC and call the function by setting 
baseMapType = "gbNRef" (resourcerer2BioC("Agilent_HumanGenome.zip", organism = 
"human", baseMapType = "gbNRef"))  

Let me know if you run into any problem. 


>Warning: cannot open file `NA'
>Warning in unifyMappings(base, eg, ug, otherSrc) :
>         Failed to get or parse Entrez Gene data because of:
> Error in file(con, "r") : unable to open connection
>The missing file in question is the parser from Genbank to Entrez Gene
>(The Agilent annotations are based on GenBank).
>> getBaseParsers("gb")
>                                                       LL
>                                                       UG
> "/usr/local/lib/R/library/AnnBuilder/scripts/gbUGParser"
>I've convinced it to use the LocusLink parser instead as the IDs should
>be the same, and the code runs for about an hour and at the very end:
>exiting from: ABPkgBuilder(baseFile, srcUrls, baseMapType, otherSrc,
>    pkgPath, organism, version, makeXML, author, fromWeb)
>Warning: cannot open compressed file
>Error in open.connection(con, "rb") : unable to open connection
>At which point I assume I'll need a proper parser for it. Any
>suggestions on what to do next?
>Having since learned my lesson:
>> sessionInfo()
>R version 2.0.0, 2004-10-04, x86_64-unknown-linux-gnu
>attached base packages:
>[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
>[7] "datasets"  "base"
>other attached packages:
>Resourcerer  AnnBuilder    annotate         XML     Biobase
>    "1.1.0"    "1.5.12"     "1.5.1"    "0.95-6"     "1.5.0"
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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