Provided by: libbio-perl-perl_1.7.6-3_all bug

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 v5.30.0                                2019-11-Bio::SearchIO::Writer::ResultTableWriter(3pm)