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Bio::SearchIO::Writer:UserTContributedBPo::SearchIO::Writer::HitTableWriter(3)

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

perl v5.24.1			  2017Bio::SearchIO::Writer::HitTableWriter(3)

NAME | SYNOPSIS | DESCRIPTION | TODO | FEEDBACK | AUTHOR | COPYRIGHT | DISCLAIMER | SEE ALSO | METHODS

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