Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

       Bio::SearchIO::Writer::HitTableWriter - Tab-delimited data for Bio::Search::Hit::HitI
       objects

SYNOPSIS

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

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

           my $writer = Bio::SearchIO::Writer::HitTableWriter->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::HitTableWriter;

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

           my $writer = Bio::SearchIO::Writer::HitTableWriter->new(
                                         -columns => [qw(
                                                         query_name
                                                         query_length
                                                         hit_name
                                                         hit_length
                                                         frac_identical_query
                                                         expect
                                                         )]  );

           my $out = Bio::SearchIO->new( -writer => $writer,
                                         -file   => ">searchio.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 HitTableWriter
       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::HitTableWriter->new(
                                      -columns => [qw( query_name
                                                       query_length
                                                       hit_name
                                                       hit_length  )],
                                      -labels  => { 1 => 'QUERY_GI',
                                                    3 => 'HIT_IDENTIFIER' } );

DESCRIPTION

       Bio::SearchIO::Writer::HitTableWriter outputs summary data for each Hit within a search
       result. Output is in tab-delimited format, one row per Hit.

       The reason why this is considered summary data is that if a hit contains multiple HSPs,
       the HSPs will be tiled and the data represents a summary across all HSPs.  See below for
       which columns are affected.  See the docs in Bio::Search::Hit::BlastHit
        for more details on HSP tiling.

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

           query_name             # Sequence identifier of the query.
           query_length           # Full length of the query sequence
           hit_name               # Sequence identifier of the hit
           hit_length             # Full length of the hit sequence
           round                  # Round number for hit (PSI-BLAST)
           expect                 # Expect value for the alignment
           score                  # Score for the alignment (e.g., BLAST score)
           bits                   # Bit score for the alignment
           num_hsps               # Number of HSPs (not the "N" value)
           frac_identical_query*  # fraction of identical substitutions in query
           frac_identical_hit*    # fraction of identical substitutions in hit
           frac_conserved_query*  # fraction of conserved substitutions in query
           frac_conserved_hit*    # fraction of conserved substitutions in hit
           frac_aligned_query*    # fraction of the query sequence that is aligned
           frac_aligned_hit*      # fraction of the hit sequence that is aligned
           length_aln_query*      # Length of the aligned portion of the query sequence
           length_aln_hit*        # Length of the aligned portion of the hit sequence
           gaps_query*            # Number of gap characters in the aligned query sequence
           gaps_hit*              # Number of gap characters in the aligned hit sequence
           gaps_total*            # Number of gap characters in the aligned query and hit sequences
           start_query*           # Starting coordinate of the aligned portion of the query sequence
           end_query*             # Ending coordinate of the aligned portion of the query sequence
           start_hit*             # Starting coordinate of the aligned portion of the hit sequence
           end_hit*               # Ending coordinate of the aligned portion of the hit sequence
           strand_query           # Strand of the aligned query sequence
           strand_hit             # Strand of the aligned hit sequence
           frame                  # Frame of the alignment (0,1,2)
           ambiguous_aln          # Ambiguous alignment indicator ('qs', 'q', 's')
           hit_description        # Full description of the hit sequence
           query_description      # Full description of the query sequence
           rank                   # The rank order of the hit
           num_hits               # Number of hits for the query finding this hit

       Items marked with a "*" report data summed across all HSPs after tiling them to avoid
       counting data from overlapping regions multiple times.

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

TODO

       Figure out the best way to incorporate algorithm-specific score columns.  The best route
       is probably to have algorithm-specific subclasses (e.g., BlastHitTableWriter,
       FastaHitTableWriter).

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, 2002 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::ResultTableWriter

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::BlastResult 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 BlastResult object. Some data is summed across multiple HSPs.
                  :
        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