Re: [Cg-pipeline-users] db3 files

[Lee K. <ls...@gm...>]

I agree that it is weird that it is taking so long.  I am querying Jay who
might be able to put an older db3 and its partner BLAST database on the
website.

I multithreaded the script for parsing the database in source control (URL
is below).  I don't think that anyone outside of our team has used it yet,
but it's ready for some beta testing.  Give it a try.  I think it requires
Perl >=5.10 with multithreading.  To get started, download it to your
normal scripts directory and run it with -h for usage information, or just
supply the xml files.

run_annotation_parse_uniprot_xml.pl -h
run_annotation_parse_uniprot_xml.pl uniprot_sprot.xml uniprot_trembl.xml #
while in your data directory


http://sourceforge.net/p/cg-pipeline/code/364/tree/cg_pipeline/branches/lkatz/scripts/run_annotation_parse_uniprot_xml.pl


On Thu, Dec 13, 2012 at 2:35 AM, Laure QUINTRIC
<Lau...@if...>wrote:

> Hello,
> Since last friday, I'm waiting for cgpipeline.db3 and
> cgpipeline.evidence.db3 to be created, and today it's only :
> run_annotation_parse_uniprot_xml.pl: main::main: [63%] Processed
> 17132000 records...
>
> Is it possible to download somewhere (ftp?) your last annotation db3
> files ? As I need them for Monday... I'm not sure I will reach 100%
> until then.
>
> Thanks a lot
> Laure
>
>
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-- 
Lee Katz, Ph.D.