[BioC] ABPkgBuilder trouble

[Nianhua Li]

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