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Bio::SearchIO::Writer::TextResultWriter.3pm

NAME

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

SYNOPSIS

   use Bio::SearchIO;
   use Bio::SearchIO::Writer::TextResultWriter;
 
   my $in = Bio::SearchIO->new(-format => 'blast',
                              -file   => shift @ARGV);
 
   my $writer = Bio::SearchIO::Writer::TextResultWriter->new();
   my $out = 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 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 Bio::Search::HSP::HSPI, Bio::Search::Hit::HitI, and 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 = 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 = Bio::SearchIO::Writer::TextResultWriter->new(
        -filters => { 'HSP' =E<gt> \&hsp_filter }  
       );
 
 

See 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 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:

   http://bugzilla.open-bio.org/
 
 

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 = Bio::SearchIO::Writer::TextResultWriter->new();
  Function: Builds a new Bio::SearchIO::Writer::TextResultWriter object 
  Returns : 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 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 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 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 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<Bio::Search::Result::ResultI> to reference
 
 

Methods Bio::SearchIO::SearchWriterI

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
 
 

no_wublastlinks

  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)