[BioC] missing AnnBuilder parser

[Francois Pepin]

Hi everyone,

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")

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
"/usr/local/lib/R/library/AnnBuilder/scripts/egAccParser"
                                                       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:

...
[21]
"/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHsWgREFSEQ.rda"
[22]
"/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHsWgSYMBOL.rda"
[23]
"/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHsWgUNIGENE.rda"
exiting from: ABPkgBuilder(baseFile, srcUrls, baseMapType, otherSrc,
pkgName,
    pkgPath, organism, version, makeXML, author, fromWeb)
Warning: cannot open compressed file
`/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHsWgLOCUSID.rda'
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"

Francois