[Bioperl-l] Entrez Gene parser questions

Mingyi Liu mingyi.liu at gpc-biotech.com
Thu Jun 9 15:11:19 EDT 2005

Law, Annie wrote:

>Just some questions about getting rid of bioperl 1.4.  Am I correct in thinking that to 'uninstall' there is no such Uninstall command but I would just delete the /usr/lib/perl5/site_perl/5.8.0/Bio  ie. The Bio directory and then Use CPAN to install bioperl 1.5
AFAIK, bioperl installer does not support uninstall.  So just delete the 
directory containing the modules and install 1.5 should work for you.

>I am running my simple script and some print statements and it takes about 10 minutes to print 2000 Entrez gene Ids.  How long does it generally take the parser to finish for example the Homo sapiens file? My real goal is not just to print but I just wanted to do a test run.  Is this about the same performance others are getting or are there some other options to speed it up?
That sounds exceedingly slow.  What type of machine are you using?  
Using Bio::ASN1::EntrezGene version 1.09 on my Intel Xeon 2.4 GHz 
machine it takes about 17 minutes to process all human records (~145000 
records).  Stefan had stated that Bio::SeqIO::entrezgene.pm is about 4 
fold slower after all the bioperl object initiations etc., so it should 
translate to 20,000+ records for 10 minutes.  If the genes you processed 
are all of 'live' status, then the speed would be slower since they have 
more content on average, but 2000 for 10 minutes still sounds slow.  
There might be some thing in your script that can be improved or scripts 
just run slowly on your machine?  Or the genes you selected on averge 
have much more content than other overall human records.

BTW, just got Stefan's mail which confirmed the speed stats above.


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