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

> >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. You have used a wrong parser. There are parsers, such as egRefseqParser and gbNRef2LLParser, that handles RefSeq ids with undersores. You need to pick one that fits your data. > >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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

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 -----Urspr?ngliche 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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

> >Your right, my problem is bound to the mix of accession and RefSeq Ids so >being correct gbUGParser wouldn't be expectd to find the refseqs (my >description of "accessions including underscores" was pretty dopey, I >admitt). I just, probably in an attack of wild speculation, thought the "gb" >scipts would automatically include the refseqs because there are no >REF2xxxParsers and the gbNRef2LLParser is the only parser with refseq on the >input side (as far as I can remember).The gbNRef2LLParser returns LocusLink >Ids but I would like to match unigene ids and there seems to be no >"gbNREF2UGParser"... >So probably I should rename a copy of the gbUGParser to "gbNREF2UGParser" >and add the "_" to regular expression. Yes, you can always write your own parsers to meet special requirements. > > >Regards, > >Benjamin > > > > > > > > >-----Urspr?ngliche Nachricht----- >Von: John Zhang [mailto:jzhang at jimmy.harvard.edu] >Gesendet: 17 January 2007 15:12 >An: bioconductor at stat.math.ethz.ch; b.otto at uke.uni-hamburg.de >Betreff: Re: [BioC] AnnBuilders paseData() doesn't recognize ACCs with >underscore? > > >> >>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. > >You have used a wrong parser. There are parsers, such as egRefseqParser and >gbNRef2LLParser, that handles RefSeq ids with undersores. You need to pick >one that fits your data. > >> >>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 >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >>Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor > >Jianhua Zhang >Department of Medical Oncology >Dana-Farber Cancer Institute >44 Binney Street >Boston, MA 02115-6084 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084