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

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.

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