[BioC] ABPkgBuilder trouble

[Johan Lindberg]

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