[BioC] athPkgBuilder

[Tine Casneuf]

Hi,

I am trying to use AnnBuilder to build a annotation package for the 
Arabidopsis ATH1 array. The athPkgBuilder function in AnnBuilder doesn't 
work properly because one of the files is no longer available from TAIRs 
ftp server.

Of the files that this function looks for:
fileExt = list(
                            estAssign = 
"Genes/est_mapping/est.Assignment.Locus",
                            seqGenes = "Genes/TAIR_sequenced_genes",
                            go = 
"Ontologies/Gene_Ontology/ATH_GO_GOSLIM.20050827.txt",
                            aliases = "Genes/gene_aliases.20041105",
                            pathway = "Pathways/aracyc_dump_20050412",
                            pmid = 
"Genes/Gene_Anatomy/ATH_Anatomy.20040209.txt"),
                        
the last one, ATH_Anatomy.20040209.txt, is no longer available.

Because the PMIDs are also available in the GO file, I removed the pmid 
parameters from the list and changed the go parameters to these yesterday:

fileExt = list(....  go = 
"Ontologies/Gene_Ontology/ATH_GO_GOSLIM.20060805.txt" ...)
ncols = list(...  go = 12...)
cols2Keep = list( ... go = c(1, 5, 9, 10)...  )
colNames = list(....  go = c("ACCNUM", "GO", "EVID", "PMID"),  ...)

but some of the environments in the package didn't build properly, so I 
can't use those.

Does anyone by any change maybe have an updated, correct version of this 
function?

Many thanks in advance,

Tine