Bio::Factory::BlastHitFactory - Factory for Bio::Search::Hit::BlastHit objects
use Bio::Factory::BlastHitFactory; my $hit_fact = Bio::Factory::BlastHitFactory->new(); my $hit = $hit_fact->create_hit( %parameters );
See documentation for create_hit() for information about %parameters.
%parameters
This module encapsulates code for creating Bio::Search::Hit::BlastHit and Bio::Search::HSP::BlastHSP objects from traditional BLAST report data (i.e., non-XML formatted).
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Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/
Steve Chervitz <sac@bioperl.org>
See the FEEDBACK section for where to send bug reports and comments.
Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
This software is provided "as is" without warranty of any kind.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : create_hit Usage : $hit = $factory->create_hit( %params ); Function: Creates a new Bio::Search::Hit::BlastHit object given raw BLAST report data, formatted in traditional BLAST report format. Returns : A single Bio::Search::Hit::BlastHit object Args : Named parameters to be passed to the BlastHit object. Parameter keys are case-insensitive. See Bio::Search::Hit::BlastHit::new() documentation for details about these parameters. The only additional parameter required is: -RESULT => a Bio::Search::Result::BlastResult object. From this result object, the program, query length, and iteration are obtained and passed on to the BlastHit.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.