[BioC] AnnBuilder package: problem with basefile type of

Nianhua Li nli at fhcrc.org
Tue Jul 25 01:33:48 CEST 2006

Hi, Weijun,

Thanks for the information. It is a bug. The code uses
"ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz" for refseq to Entrez
Gene mapping. It should use "gene2refseq.gz" instead. The bug has been fixed and
version number increased to 1.11.5. The update is available on svn now, and will
be available on web at around 1pm, July 26 (Pacific Time). If you are in a
hurry, this is the modification:
--- ABPkgBuilder.R      (v1.11.4)
+++ ABPkgBuilder.R      (v1.11.5)
@@ -558,11 +557,12 @@

 getUniMappings <- function(baseName, eg, ug, otherSrc, baseMapType){
     base <- getBaseFile(baseName)

     if(baseMapType == "refseq"){
-        unified <- unifyMappings(base, eg, NULL, otherSrc)
+       eg_refseq <- eg
+       eg_refseq at accession <- eg_refseq at refseq
+        unified <- unifyMappings(base, eg_refseq, NULL, otherSrc)
     }else if(baseMapType != "ll"){
         #ug <- UG(srcUrl = srcUrl(ug),
         #         parser = parser(ug), baseFile = baseName(ug),

Also, notice that the ACCNUM environment generated by AnnBuilder is a copy of
your input, not probe-to-GenBank mapping. ABPkgBuilder doesn't provide
probe-to-GenBank mapping unless baseFile contains that information.

hope it works this time :P


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