NAME

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

SYNOPSIS

        use Bio::Tools::Run::Alignment::Blat;
        my $factory = Bio::Tools::Run::Alignment::Blat->new(-db => $database);
        # $report is a Bio::SearchIO-compliant object
        my $report = $factory->run($seqobj);

DESCRIPTION

       Wrapper module for Blat program. This newer version allows for all parameters to be set by
       passing them as an option to new().

       Key bits not implemented yet (TODO):

       •  Implement all needed Bio::Tools::Run::WrapperBase methods

          Missing are a few, including version().

       •  Re-implement using IPC::Run

          Would like to get this running under something less reliant on OS-dependent changes
          within code.

       •  No .2bit or .nib conversions yet

          These require callouts to faToNib or faTwoTwoBit, which may or may not be installed on
          a user's machine.  We can possibly add functionality to check for faToTwoBit/faToNib
          and other UCSC tools in the future.

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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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://redmine.open-bio.org/projects/bioperl/

AUTHOR

        Chris Fields - cjfields at bioperl dot org

        Original 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 _

   new
        Title   : new
        Usage   : $blat->new( -db => '' )
        Function: Create a new Blat factory
        Returns : A new Bio::Tools::Run::Alignment::Blat object
        Args    : -db       : Mandatory parameter. See db()
                  -qsegment : see qsegment()
                  -tsegment : see tsegment()
                  Also, Blat parameters and flags are accepted: -t, -q, -minIdentity,
                     -minScore, -out, -trimT, ...
                  See Blat's manual for details.

   program_name
        Title   : program_name
        Usage   : $factory->program_name()
        Function: Get 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    :

   run
        Title   : run()
        Usage   : $obj->run($query)
        Function: Run Blat.
        Returns : A Bio::SearchIO object that holds the results
        Args    : A Bio::PrimarySeqI object or a file of query sequences

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

   db
        Title   : db
        Usage   : $obj->db()
        Function: Get or set the file of database sequences (.fa , .nib or .2bit)
        Returns : Database filename
        Args    : Database filename

   qsegment
        Title    : qsegment
        Usage    : $obj->qsegment('sequence_a:0-1000')
        Function : pass in a B<UCSC-compliant> string for the query sequence(s)
        Returns  : string
        Args     : string
        Note     : Requires the sequence(s) in question be 2bit or nib format
        Reminder : UCSC segment/regions coordinates are 0-based half-open (sequence
                   begins at 0, but start isn't counted with length), whereas BioPerl
                   coordinates are 1-based closed (sequence begins with 1, both start
                   and end are counted in the length of the segment). For example, a
                   segment that is 'sequence_a:0-1000' will have BioPerl coordinates of
                   'sequence_a:1-1000', both with the same length (1000).

   tsegment
        Title    : tsegment
        Usage    : $obj->tsegment('sequence_a:0-1000')
        Function : pass in a B<UCSC-compliant> string for the target sequence(s)
        Returns  : string
        Args     : string
        Note     : Requires the sequence(s) in question be 2bit or nib format
        Reminder : UCSC segment/regions coordinates are 0-based half-open (sequence
                   begins at 0, but start isn't counted with length), whereas BioPerl
                   coordinates are 1-based closed (sequence begins with 1, both start
                   and end are counted in the length of the segment). For example, a
                   segment that is 'sequence_a:0-1000' will have BioPerl coordinates of
                   'sequence_a:1-1000', both with the same length (1000).

   outfile_name
        Title    : outfile_name
        Usage    : $obj->outfile_name('out.blat')
        Function : Get or set the name for the BLAT output file
        Returns  : string
        Args     : string

   searchio
        Title    : searchio
        Usage    : $obj->searchio{-writer => $writer}
        Function : Pass in additional parameters to the returned Bio::SearchIO parser
        Returns  : Hash reference with Bio::SearchIO parameters
        Args     : Hash reference
        Note     : Currently, this implementation overrides any passed -format
                   parameter based on whether the output is changed ('out').  This
                   may change if requested, but we can't see the utility of doing so,
                   as requesting mismatched output/parser combinations is just a recipe
                   for disaster

Bio::ParameterBaseI-specific methods

       These methods are part of the Bio::ParameterBaseI interface

   set_parameters
        Title   : set_parameters
        Usage   : $pobj->set_parameters(%params);
        Function: sets the parameters listed in the hash or array
        Returns : None
        Args    : [optional] hash or array of parameter/values.  These can optionally
                  be hash or array references
        Note    : This only sets parameters; to set methods use the method name

   reset_parameters
        Title   : reset_parameters
        Usage   : resets values
        Function: resets parameters to either undef or value in passed hash
        Returns : none
        Args    : [optional] hash of parameter-value pairs

   validate_parameters
        Title   : validate_parameters
        Usage   : $pobj->validate_parameters(1);
        Function: sets a flag indicating whether to validate parameters via
                  set_parameters() or reset_parameters()
        Returns : Bool
        Args    : [optional] value evaluating to True/False
        Note    : NYI

   parameters_changed
        Title   : parameters_changed
        Usage   : if ($pobj->parameters_changed) {...}
        Function: Returns boolean true (1) if parameters have changed
        Returns : Boolean (0 or 1)
        Args    : None
        Note    : This module does not run state checks, so this always returns True

   available_parameters
        Title   : available_parameters
        Usage   : @params = $pobj->available_parameters()
        Function: Returns a list of the available parameters
        Returns : Array of parameters
        Args    : [optional] name of executable being used; defaults to returning all
                  available parameters

   get_parameters
        Title   : get_parameters
        Usage   : %params = $pobj->get_parameters;
        Function: Returns list of set key-value pairs, parameter => value
        Returns : List of key-value pairs
        Args    : none

to_* methods

       All to_* methods are implementation-specific

   to_exe_string
        Title   : to_exe_string
        Usage   : $string = $pobj->to_exe_string;
        Function: Returns string (command line string in this case)
        Returns : String
        Args    :