Using NCBI Blast remotely via bioperl - Using NCBI Blast remotely via bioperl (Jan/06/2005 )
Hi, I am using bioperl to connect to NCBI blast remotely using "RemoteBlast". I could get "rid" for example "1105021865-30641-185846961593.BLASTQ4". But i could not get any result. From the below code,
my $rc = $factory->retrieve_blast($rid);
I tried to print $rc which returns '-1'.
Any help is appreciated. Thanks.
Also i would like to use 'webblast.pm'. Has anyone used it before? Thanks.
If $rc is -1 there is an error and it could not retrieve the result. In Bioperl < 1.5.1 you would get back a Bio::Tools::BPlite object by default or in Bioperl 1.5.1 you get a Bio::SearchIO object by default. You will want to run it in verbose mode with this code:
From the API documentation about retrieve_blast:
Title : retrieve_blast
Usage : my $blastreport = $blastfactory->retrieve_blast($rid);
Function: Attempts to retrieve a blast report from remote blast queue
Returns : -1 on error,
0 on 'job not finished',
Bio::Tools::BPlite or Bio::Tools::Blast object
(depending on how object was initialized) on success
Args : Remote Blast ID (RID)
Also, much work was done recently to better handle RemoteBlast so upgrade to Bioperl 1.5.1
In the future I'd also suggest asking your questions on the Bioperl mailing list as you'll be a better answer response time.