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FAST-1.06
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/ FAST::Bio::SearchIO::Writer::TextResultWriter

NAME

FAST::Bio::SearchIO::Writer::TextResultWriter - Object to implement writing a FAST::Bio::Search::ResultI in Text.

SYNOPSIS

  use FAST::Bio::SearchIO;
  use FAST::Bio::SearchIO::Writer::TextResultWriter;

  my $in = FAST::Bio::SearchIO->new(-format => 'blast',
			     -file   => shift @ARGV);

  my $writer = FAST::Bio::SearchIO::Writer::TextResultWriter->new();
  my $out = FAST::Bio::SearchIO->new(-writer => $writer);
  $out->write_result($in->next_result);

DESCRIPTION

This object implements the SearchWriterI interface which will produce a set of Text for a specific FAST::Bio::Search::Report::ReportI interface.

You can also provide the argument -filters => \%hash to filter the at the hsp, hit, or result level. %hash is an associative array which contains any or all of the keys (HSP, HIT, RESULT). The values pointed to by these keys would be references to a subroutine which expects to be passed an object - one of FAST::Bio::Search::HSP::HSPI, FAST::Bio::Search::Hit::HitI, and FAST::Bio::Search::Result::ResultI respectively. Each function needs to return a boolean value as to whether or not the passed element should be included in the output report - true if it is to be included, false if it to be omitted.

For example to filter on sequences in the database which are too short for your criteria you would do the following.

Define a hit filter method

sub hit_filter { 
    my $hit = shift;
    return $hit->length E<gt> 100; # test if length of the hit sequence
                                   # long enough    
}
my $writer = FAST::Bio::SearchIO::Writer::TextResultWriter->new(
     -filters => { 'HIT' =E<gt> \&hit_filter }  
    );

Another example would be to filter HSPs on percent identity, let's only include HSPs which are 75% identical or better.

sub hsp_filter {
    my $hsp = shift;
    return $hsp->percent_identity E<gt> 75;
}
my $writer = FAST::Bio::SearchIO::Writer::TextResultWriter->new(
    -filters => { 'HSP' =E<gt> \&hsp_filter }  
   );

See FAST::Bio::SearchIO::SearchWriterI for more info on the filter method.

This module will use the module Text::Wrap if it is installed to wrap the Query description line. If you do not have Text::Wrap installed this module will work fine but you won't have the Query line wrapped. You will see a warning about this when you first instantiate a TextResultWriter - to avoid these warnings from showing up, simply set the verbosity upon initialization to -1 like this: my $writer = new FAST::Bio::SearchIO::Writer::TextResultWriter(-verbose => -1);

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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:

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

AUTHOR - Jason Stajich

Email jason@bioperl.org

APPENDIX

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

new

Title   : new
Usage   : my $obj = FAST::Bio::SearchIO::Writer::TextResultWriter->new();
Function: Builds a new FAST::Bio::SearchIO::Writer::TextResultWriter object 
Returns : FAST::Bio::SearchIO::Writer::TextResultWriter
Args    : -filters => hashref with any or all of the keys (HSP HIT RESULT)
          which have values pointing to a subroutine reference
          which will expect to get a Hit,HSP, Result object respectively
          -no_wublastlinks => boolean. Do not display WU-BLAST lines even if 
                              they are parsed out
                              Links = (1)

to_string

Purpose   : Produces data for each Search::Result::ResultI in a string.
          : This is an abstract method. For some useful implementations,
          : see ResultTableWriter.pm, HitTableWriter.pm, 
          : and HSPTableWriter.pm.
Usage     : print $writer->to_string( $result_obj, @args );
Argument  : $result_obj = A FAST::Bio::Search::Result::ResultI object
          : @args = any additional arguments used by your implementation.
Returns   : String containing data for each search Result or any of its
          : sub-objects (Hits and HSPs).
Throws    : n/a

start_report

Title   : start_report
Usage   : $index->start_report( CODE )
Function: Stores or returns the code to
          write the start of the <HTML> block, the <TITLE> block
          and the start of the <BODY> block of HTML.   Useful
          for (for instance) specifying alternative
          HTML if you are embedding the output in
          an HTML page which you have already started.
          (For example a routine returning a null string).
          Returns \&default_start_report (see below) if not
          set. 
Example : $index->start_report( \&my_start_report )
Returns : ref to CODE if called without arguments
Args    : CODE

default_start_report

Title   : default_start_report
Usage   : $self->default_start_report($result)
Function: The default method to call when starting a report.
Returns : sting
Args    : First argument is a FAST::Bio::Search::Result::ResultI

title

Title   : title
Usage   : $self->title($CODE)

 Function: Stores or returns the code to provide HTML for the given
           BLAST report that will appear at the top of the BLAST report
           HTML output.  Useful for (for instance) specifying
           alternative routines to write your own titles.
           Returns \&default_title (see below) if not
           set. 
 Example : $index->title( \&my_title )
 Returns : ref to CODE if called without arguments
 Args    : CODE

default_title

Title   : default_title
Usage   : $self->default_title($result)
Function: Provides HTML for the given BLAST report that will appear
          at the top of the BLAST report output.
Returns : empty for text implementation
Args    : First argument is a FAST::Bio::Search::Result::ResultI

introduction

Title   : introduction
Usage   : $self->introduction($CODE)

 Function: Stores or returns the code to provide HTML for the given
           BLAST report detailing the query and the
           database information.
           Useful for (for instance) specifying
           routines returning alternative introductions.
           Returns \&default_introduction (see below) if not
           set. 
 Example : $index->introduction( \&my_introduction )
 Returns : ref to CODE if called without arguments
 Args    : CODE

default_introduction

Title   : default_introduction
Usage   : $self->default_introduction($result)
Function: Outputs HTML to provide the query
          and the database information
Returns : string containing HTML
Args    : First argument is a FAST::Bio::Search::Result::ResultI
          Second argument is string holding literature citation

end_report

Title   : end_report
Usage   : $self->end_report()
Function: The method to call when ending a report, this is
          mostly for cleanup for formats which require you to 
          have something at the end of the document (</BODY></HTML>)
          for HTML
Returns : string
Args    : none

id_parser

Title   : id_parser
Usage   : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
          parse the ID for record from a string.  Useful
          for (for instance) specifying a different
          parser for different flavours of FASTA file. 
          Returns \&default_id_parser (see below) if not
          set. If you supply your own id_parser
          subroutine, then it should expect a fasta
          description line.  An entry will be added to
          the index for each string in the list returned.
Example : $index->id_parser( \&my_id_parser )
Returns : ref to CODE if called without arguments
Args    : CODE

default_id_parser

Title   : default_id_parser
Usage   : $id = default_id_parser( $header )
Function: The default Fasta ID parser for Fasta.pm
          Returns $1 from applying the regexp /^>\s*(\S+)/
          to $header.
Returns : ID string
Args    : a fasta header line string

algorithm_reference

Title   : algorithm_reference
Usage   : my $reference = $writer->algorithm_reference($result);
Function: Returns the appropriate Bibliographic reference for the 
          algorithm format being produced
Returns : String
Args    : L<FAST::Bio::Search::Result::ResultI> to reference

Methods FAST::Bio::SearchIO::SearchWriterI

FAST::Bio::SearchIO::SearchWriterI inherited methods.

filter

Title   : filter
Usage   : $writer->filter('hsp', \&hsp_filter);
Function: Filter out either at HSP,Hit,or Result level
Returns : none
Args    : string => data type,
          CODE reference
Title   : no_wublastlinks
Usage   : $obj->no_wublastlinks($newval)
Function: Get/Set boolean value regarding whether or not to display
          Link = (1) 
          type output in the report output (WU-BLAST only)
Returns : boolean
Args    : on set, new boolean value (a scalar or undef, optional)