NAME

Bio::Tools::Run::Blat

SYNOPSIS

  Build a Blat  factory

  my $factory = Bio::Tools::Run::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://bio.perl.org/MailList.html             - 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
 email or the web:

 bioperl-bugs@bioperl.org
 http://bugzilla.bioperl.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, obtiained from ENV variable.
 Returns:  string
 Args    :

new

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

_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    :

cpanm Bio::Factory::EMBOSS

perl -MCPAN -e shell
install Bio::Factory::EMBOSS