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

NAME

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

SYNOPSIS

Example 1: Using the default columns

use FAST::Bio::SearchIO;
use FAST::Bio::SearchIO::Writer::ResultTableWriter;

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

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

my $out = FAST::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 FAST::Bio::SearchIO;
    use FAST::Bio::SearchIO::Writer::ResultTableWriter;

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

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

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

DESCRIPTION

FAST::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 FAST::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: FAST::Bio::SearchIO::Writer::HitTableWriter or FAST::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 FAST::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://redmine.open-bio.org/projects/bioperl/

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

FAST::Bio::SearchIO::Writer::HitTableWriter, FAST::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 FAST::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