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    :

cpanm Bio::Factory::EMBOSS

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