Bio::Tools::Run::Alignment::Blat(3pm)

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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

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_exe_string

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