Christopher Fields > BioPerl-1.6.920 > Bio::SearchIO::Writer::ResultTableWriter

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Module Version: 1.006920   Source   Latest Release: BioPerl-1.6.924

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://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 ^

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
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