[Bioperl-l] getting the Sbjct database from a hit

Catherine Letondal letondal@pasteur.fr
Fri, 06 Oct 2000 14:30:20 +0200


I have a script that extracts sequences from a blast report which doesn't work 
anymore. The sequences were extracted giving the name of the subject database and its 
AC. There is a change apparently, since with the last bioperl version this doesn't work
anymore :

    foreach $hit ($blast->hits) {
	$db = $hit->database;

What is the new way to do this (there is apparently a Bio::Tools::Blast::Sbjct
which has the ->database method, but I don't know how to create from - what's is
this @hitdata in the doc. example (http://bioperl.org/Core/POD//Bio/Tools/Blast/Sbjct.html):
    require Bio::Tools::Blast::Sbjct;
    $hit = new Bio::Tools::Blast::Sbjct (-DATA    =>\@hitData, 
                                         -PARENT  =>$self, 
                                         -NAME    =>5,
                                         -RANK    =>5,
                                         -RANK_BY =>'order',
                                         -MAKE    =>'query' (or 'sbjct'),
                                         -OVERLAP =>2,
                                         -PROGRAM =>'TBLASTN'

Many thanks for any help,

Catherine Letondal -- Pasteur Institute Computing Center