Hi all, Ill revoke a thred from Mars that I found a solution to when  
trying the same thing again just in case anyone else runs into the  
same problem.

Im using mac os X.

My main problem was that I couldnt get ABPkgBuilder to work with my  
chip due to (at least I thought so) Perl locale handling. I got  
warnings such as

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.
perl: warning: Falling back to the standard locale ("C")

but the problem was that when saving a file to .txt format using mac  
os X you get mac line endings (\r) instead of unix line endings (\n).  
This will make the script egAccParser.pl fail to map genbank  
accession numbers to gene ID:s. So one line code of perl

perl -pi -e 's/\r/\n/g' <filename>

will convert your line endings and ABPkgBuilder will work.

Best regards

// Johan


On Mar 6, 2007, at 6:42 PM, Nianhua Li wrote:

> 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


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