/ 
bioperl-run-1.5.2_100
/ Bio::Tools::Run::Alignment::Blat

NAME

Bio::Tools::Run::Alignment::Blat

SYNOPSIS

Build a Blat factory.

use Bio::Tools::Run::Alignment::Blat;

my $factory = Bio::Tools::Run::Alignment::Blat->new();

# Pass the factory a Bio::Seq object
# @feats is an array of Bio::SeqFeature::Generic objects
my @feats = $factory->run($seq,$DB);

DESCRIPTION

Wrapper module for Blat program

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHOR - Bala

Email bala@tll.org.sg

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

program_name

Title   : program_name
Usage   : $factory->program_name()
Function: holds the program name
Returns : string
Args    : None

program_dir

Title   : program_dir
Usage   : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns : string
Args    :

new

Title   : new
Usage   : $blat->new(@params)
Function: creates a new Blat factory
Returns : Bio::Tools::Run::Alignment::Blat
Args    :

run

Title   :   run()
Usage   :   $obj->run($query)
Function:   Runs Blat and creates an array of featrues
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :   A Bio::PrimarySeqI

align

Title   :   align
Usage   :   $obj->align($query)
Function:   Alias to run()

_input

Title   :   _input
Usage   :   obj->_input($seqFile)
Function:   Internal (not to be used directly)
Returns :
Args    :

_database

Title   :   _database
Usage   :   obj->_database($seqFile)
Function:   Internal (not to be used directly)
Returns :
Args    :

_run

Title   :   _run
Usage   :   $obj->_run()
Function:   Internal (not to be used directly)
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :

_writeSeqFile

Title   :   _writeSeqFile
Usage   :   obj->_writeSeqFile($seq)
Function:   Internal (not to be used directly)
Returns :
Args    :