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Bio::SearchIO::Writer:UseruContributed:PerlchIO::Writer::ResultTableWriter(3)

NAME
       Bio::SearchIO::Writer::ResultTableWriter	- Outputs tab-delimited	data
       for each	Bio::Search::Result::ResultI object.

SYNOPSIS
   Example 1: Using the	default	columns
	   use Bio::SearchIO;
	   use Bio::SearchIO::Writer::ResultTableWriter;

	   my $in = Bio::SearchIO->new();

	   my $writer =	Bio::SearchIO::Writer::ResultTableWriter->new();

	   my $out = Bio::SearchIO->new( -writer => $writer );

	   while ( my $result =	$in->next_result() ) {
	       $out->write_result($result, ($in->report_count -	1 ? 0 :	1) );
	   }

   Example 2: Specifying a subset of columns
	   use Bio::SearchIO;
	   use Bio::SearchIO::Writer::ResultTableWriter;

	   my $in = Bio::SearchIO->new();

	   my $writer =	Bio::SearchIO::Writer::ResultTableWriter->new(
					 -columns => [qw(
							 query_name
							 query_length
							 num_hits
							 )]  );

	   my $out = Bio::SearchIO->new( -writer => $writer,
					 -file	 => ">result.out" );

	   while ( my $result =	$in->next_result() ) {
	       $out->write_result($result, ($in->report_count -	1 ? 0 :	1) );
	   }

   Custom Labels
       You can also specify different column labels if you don't want to use
       the defaults.  Do this by specifying a "-labels"	hash reference
       parameter when creating the ResultTableWriter object.  The keys of the
       hash should be the column number	(left-most column = 1) for the
       label(s)	you want to specify. Here's an example:

	   my $writer =	Bio::SearchIO::Writer::ResultTableWriter->new(
				      -columns => [qw( query_name
						       query_length
						       query_description
						       num_hits)],
				      -labels  => { 1 => 'QUERY_GI',
						    2 => 'QUERY_LENGTH'	} );

DESCRIPTION
       Bio::SearchIO::Writer::ResultTableWriter	outputs	data in	tab-delimited
       format for each search result, one row per search result. This is a
       very coarse-grain level of information since it only includes data
       stored in the Bio::Search::Result::ResultI object itself	and does not
       include any information about hits or HSPs.

       You most	likely will never use this object but instead will use one of
       its subclasses: Bio::SearchIO::Writer::HitTableWriter or
       Bio::SearchIO::Writer::HSPTableWriter.

   Available Columns
       Here are	the columns that can be	specified in the "-columns" parameter
       when creating a ResultTableWriter object.  If a "-columns" parameter is
       not specified, this list, in this order,	will be	used as	the default.

	   query_name
	   query_length
	   query_description

       For more	details	about these columns, see the documentation for the
       corresponding method in Bio::Search::Result::ResultI.

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:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR
       Steve Chervitz <sac@bioperl.org>

       See the FEEDBACK	section	 for where to send bug reports and comments.

COPYRIGHT
       Copyright (c) 2001 Steve	Chervitz. All Rights Reserved.

       This library is free software; you can redistribute it and/or modify it
       under the same terms as Perl itself.

DISCLAIMER
       This software is	provided "as is" without warranty of any kind.

SEE ALSO
       Bio::SearchIO::Writer::HitTableWriter,
       Bio::SearchIO::Writer::HSPTableWriter

METHODS
   to_string()
       Note: this method is not	intended for direct use. The
       SearchIO::write_result()	method calls it	automatically if the writer is
       hooked up to a SearchIO object as illustrated in	the SYNOPSIS section .

	Title	  : to_string()
		  :
	Usage	  : print $writer->to_string( $result_obj, [$include_labels] );
		  :
	Argument  : $result_obj	= A Bio::Search::Result::ResultI object
		  : $include_labels = boolean, if true column labels are included (default: false)
		  :
	Returns	  : String containing tab-delimited set	of data	for each hit
		  : in a ResultI object. Some data is summed across multiple HSPs.
		  :
	Throws	  : n/a

   column_labels
	Usage	  : print $result_obj->column_labels();
	Purpose	  : Get	column labels for to_string().
	Returns	  : String containing column labels. Tab-delimited.
	Argument  : n/a
	Throws	  : n/a

   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.  Nothing for
		  a text message.
	Returns	: string
	Args	: none

   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

perl v5.24.1			  2Bio::SearchIO::Writer::ResultTableWriter(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | COPYRIGHT | DISCLAIMER | SEE ALSO | METHODS

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