[BioC] AnnBuilders paseData() doesn't recognize ACCs withunderscore?

[Benjamin Otto]

Ah, sorry, just solved the problem. I had to add the "_" to the regular
expression in the gbUGParser file in the scripts folder...

Regards,

Benjamin




-----Ursprüngliche Nachricht-----
Von: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von Benjamin Otto
Gesendet: 17 January 2007 14:50
An: bioconductor at stat.math.ethz.ch
Betreff: [BioC] AnnBuilders paseData() doesn't recognize ACCs
withunderscore?

Hi,

parseData() seems to have problems in recognition of accession numbers
including an underscore like "NM_001815". The function just doesn't find
them although they do exist in the database file.

Here is the example I'm trying to get working:

>library(AnnBuilder)
>pkgpath <- .find.package("AnnBuilder")
># unigene infos
>ugUrl <- "C:/Programme/R/R-2.4.1/library/AnnBuilder/data/Ths.data"
># parsing
>ug <- UG(srcUrl = ugUrl, parser = file.path(pkgpath, "scripts", 
>"gbUGParser"), baseFile = "geneNMap", organism = "Homo sapiens", built 
>= "N/A", fromWeb = FALSE)
>parseData(ug)

The geneNMap file has the entries:

32468_f_at	D90278;M16652
32469_at	L00693
NM_001815	NM_001815
BF897514	BF897514
38912_at	D90042
BC028014	BC028014
D90042	D90042

I get out:
		[,1]		[,2]
32468_f_at "32468_f_at" "1084;63036"
32469_at   "32469_at"   "1084"      
38912_at   "38912_at"   "10"        
BF897514   "BF897514"   "1084"      
D90042     "D90042"     "10"        


Thanks a lot for your help in advance..

Regards,

Benjamin


--
Benjamin Otto
Universitaetsklinikum Eppendorf Hamburg
Institut fuer Klinische Chemie
Martinistrasse 52
20246 Hamburg

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