ABPkgBuilder trouble
1
0
Entering edit mode
@johan-lindberg-815
Last seen 8.1 years ago
An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070305/ 78afc3d5/attachment.pl
• 630 views
ADD COMMENT
0
Entering edit mode
Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
Hi, Johan, Your perl configuration may have problem. The step of converting GenBank accessions or RefSeq accessions to Entrez Gene ids is performed by some perl scripts. The related functions are "fileMuncher" and ".callperl" in the LL.R of AnnBuilder. Once AnnBuilder gets the probe to Entrez Gene mapping, all other annotations are retrieved by pure R functions. Therefore I guess your perl may have problem. In your previous post, I observe this warning: perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LC_ALL = (unset), LANG = "en_SE.UTF-8" are supported and installed on your system. And your sessionInfo was: > sessionInfo() R version 2.4.1 (2006-12-18) i386-apple-darwin8.8.1 locale: C This may be related to the problem. I am sure there are perl experts on the list and they can provide very useful suggestions. To separate the perl problem from the AnnBuilder puzzle, please try the following on your machine: 1. create a empty folder, say <tmp> 2. copy your probe-to-GenBank mapping file ("C:/Annb/humOligoV3.0.2.txt" ?) to <tmp> and rename to myinput.txt 3. download ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz to <tmp>, and unzip it to gene2accession. 4. create an empty file named myoutput.txt 5. copy AnnBuilder/scripts/egAccParser to <tmp> and rename to egAccParser.pl 6. add the following lines to the beginning of egAccParser.pl: ----------------------------------------------------- #!/usr/bin/perl open(BASE, "<myinput.txt") ||="" die="" "can="" not="" open="" myinput.txt";="" open(data,="" "<gene2accession")="" ||="" die="" "can="" not="" open="" gene2accession";="" open(out,="" "="">myoutput.txt") || die "Can not open myoutput.txt"; ------------------------------------------------------ 7. from <tmp>, run: perl egAccParser.pl If everything works find, myoutput.txt should contain probe-to-Entrez Gene mapping. hope this is helpful nianhua
ADD COMMENT
0
Entering edit mode
Thank you for your help Nianhua. Its greatly appreciated. I followed your instructions and everything went according to plan except for that the script didn't write anything to myoutput.txt (its empty). So I guess this is were the problem resides, but i have no idea what to do about it. Any suggestions? Best regards // Johan Lindberg On Mar 5, 2007, at 6:54 PM, Nianhua Li wrote: > Hi, Johan, > > Your perl configuration may have problem. The step of converting > GenBank accessions or RefSeq accessions to Entrez Gene ids is > performed by some perl scripts. The related functions are > "fileMuncher" and ".callperl" in the LL.R of AnnBuilder. Once > AnnBuilder gets the probe to Entrez Gene mapping, all other > annotations are retrieved by pure R functions. Therefore I guess your > perl may have problem. In your previous post, I observe this warning: > > perl: warning: Setting locale failed. > perl: warning: Please check that your locale settings: > LC_ALL = (unset), > LANG = "en_SE.UTF-8" > are supported and installed on your system. > > And your sessionInfo was: >> sessionInfo() > R version 2.4.1 (2006-12-18) > i386-apple-darwin8.8.1 > > locale: > C > > This may be related to the problem. I am sure there are perl experts > on the list and they can provide very useful suggestions. > > To separate the perl problem from the AnnBuilder puzzle, please try > the following on your machine: > > 1. create a empty folder, say <tmp> > 2. copy your probe-to-GenBank mapping file > ("C:/Annb/humOligoV3.0.2.txt" ?) to <tmp> and rename to myinput.txt > 3. download ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz to > <tmp>, and unzip it to gene2accession. > 4. create an empty file named myoutput.txt > 5. copy AnnBuilder/scripts/egAccParser to <tmp> and rename to > egAccParser.pl > 6. add the following lines to the beginning of egAccParser.pl: > ----------------------------------------------------- > #!/usr/bin/perl > open(BASE, "<myinput.txt") ||="" die="" "can="" not="" open="" myinput.txt";=""> open(DATA, "<gene2accession") ||="" die="" "can="" not="" open="" gene2accession";=""> open(OUT, ">myoutput.txt") || die "Can not open myoutput.txt"; > ------------------------------------------------------ > 7. from <tmp>, run: perl egAccParser.pl > > If everything works find, myoutput.txt should contain probe-to- Entrez > Gene mapping. > > hope this is helpful > > nianhua
ADD REPLY
0
Entering edit mode
An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070306/ 5a69b41c/attachment.pl
ADD REPLY
0
Entering edit mode
Hi, Johan, A couple of questions/suggestions and one offer: 1. You mentioned that you have tried AnnBuilder on two windows computers. Could you try just the perl script I sent to you in my last email and tell me the result? 2. Did you see the perl warning about locale warning when you ran the perl script on your mac machine? I gooled the warning and found this http://www.xav.com/perl/lib/Pod/perllocale.html . May be fixing the locale can help? 3. I am not a perl expert but I know a bit about AnnBuilder. I am sorry that I can't help you much on the perl problem. But I can build the annotation package for you if you could send me (offline) your base file and the script you used to invoke AnnBuilder. I have a snapshot of all the source data (GO, KEGG, Entrez, etc) for release 1.9, the upcoming release 2.0. I can build annotation package with either one of them or just use the most up-to-date data online. Please let me know which one you perfer to. best nianhua
ADD REPLY

Login before adding your answer.

Traffic: 434 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6