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Bio::SearchIO::Writer:UsertContributedoPerearchIO::Writer::TextResultWriter(3)

NAME
       Bio::SearchIO::Writer::TextResultWriter - Object	to implement writing a
       Bio::Search::ResultI in Text.

SYNOPSIS
	 use Bio::SearchIO;
	 use Bio::SearchIO::Writer::TextResultWriter;

	 my $in	= Bio::SearchIO->new(-format =>	'blast',
				    -file   => shift @ARGV);

	 my $writer = Bio::SearchIO::Writer::TextResultWriter->new();
	 my $out = Bio::SearchIO->new(-writer => $writer);
	 $out->write_result($in->next_result);

DESCRIPTION
       This object implements the SearchWriterI	interface which	will produce a
       set of Text for a specific Bio::Search::Report::ReportI interface.

       You can also provide the	argument -filters => \%hash to filter the at
       the hsp,	hit, or	result level.  %hash is	an associative array which
       contains	any or all of the keys (HSP, HIT, RESULT).  The	values pointed
       to by these keys	would be references to a subroutine which expects to
       be passed an object - one of Bio::Search::HSP::HSPI,
       Bio::Search::Hit::HitI, and Bio::Search::Result::ResultI	respectively.
       Each function needs to return a boolean value as	to whether or not the
       passed element should be	included in the	output report -	true if	it is
       to be included, false if	it to be omitted.

       For example to filter on	sequences in the database which	are too	short
       for your	criteria you would do the following.

       Define a	hit filter method

	 sub hit_filter	{
	     my	$hit = shift;
	     return $hit->length E<gt> 100; # test if length of	the hit	sequence
					    # long enough
	 }
	 my $writer = Bio::SearchIO::Writer::TextResultWriter->new(
	      -filters => { 'HIT' =E<gt> \&hit_filter }
	     );

       Another example would be	to filter HSPs on percent identity, let's only
       include HSPs which are 75% identical or better.

	  sub hsp_filter {
	      my $hsp =	shift;
	      return $hsp->percent_identity E<gt> 75;
	  }
	  my $writer = Bio::SearchIO::Writer::TextResultWriter->new(
	      -filters => { 'HSP' =E<gt> \&hsp_filter }
	     );

       See Bio::SearchIO::SearchWriterI	for more info on the filter method.

       This module will	use the	module Text::Wrap if it	is installed to	wrap
       the Query description line.  If you do not have Text::Wrap installed
       this module will	work fine but you won't	have the Query line wrapped.
       You will	see a warning about this when you first	instantiate a
       TextResultWriter	- to avoid these warnings from showing up, simply set
       the verbosity upon initialization to -1 like this: my $writer = new
       Bio::SearchIO::Writer::TextResultWriter(-verbose	=> -1);

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 the
       Bioperl mailing list.  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 of
       the bugs	and their resolution. Bug reports can be submitted via the
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich
       Email jason@bioperl.org

APPENDIX
       The rest	of the documentation details each of the object	methods.
       Internal	methods	are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::SearchIO::Writer::TextResultWriter->new();
	Function: Builds a new Bio::SearchIO::Writer::TextResultWriter object
	Returns	: Bio::SearchIO::Writer::TextResultWriter
	Args	: -filters => hashref with any or all of the keys (HSP HIT RESULT)
		  which	have values pointing to	a subroutine reference
		  which	will expect to get a Hit,HSP, Result object respectively
		  -no_wublastlinks => boolean. Do not display WU-BLAST lines even if
				      they are parsed out
				      Links = (1)

   to_string
	Purpose	  : Produces data for each Search::Result::ResultI in a	string.
		  : This is an abstract	method.	For some useful	implementations,
		  : see	ResultTableWriter.pm, HitTableWriter.pm,
		  : and	HSPTableWriter.pm.
	Usage	  : print $writer->to_string( $result_obj, @args );
	Argument  : $result_obj	= A Bio::Search::Result::ResultI object
		  : @args = any	additional arguments used by your implementation.
	Returns	  : String containing data for each search Result or any of its
		  : sub-objects	(Hits and HSPs).
	Throws	  : n/a

   start_report
	 Title	 : start_report
	 Usage	 : $index->start_report( CODE )
	 Function: Stores or returns the code to
		   write the start of the <HTML> block,	the <TITLE> block
		   and the start of the	<BODY> block of	HTML.	Useful
		   for (for instance) specifying alternative
		   HTML	if you are embedding the output	in
		   an HTML page	which you have already started.
		   (For	example	a routine returning a null string).
		   Returns \&default_start_report (see below) if not
		   set.
	 Example : $index->start_report( \&my_start_report )
	 Returns : ref to CODE if called without arguments
	 Args	 : CODE

   default_start_report
	Title	: default_start_report
	Usage	: $self->default_start_report($result)
	Function: The default method to	call when starting a report.
	Returns	: sting
	Args	: First	argument is a Bio::Search::Result::ResultI

   title
	Title	: title
	Usage	: $self->title($CODE)

	 Function: Stores or returns the code to provide HTML for the given
		   BLAST report	that will appear at the	top of the BLAST report
		   HTML	output.	 Useful	for (for instance) specifying
		   alternative routines	to write your own titles.
		   Returns \&default_title (see	below) if not
		   set.
	 Example : $index->title( \&my_title )
	 Returns : ref to CODE if called without arguments
	 Args	 : CODE

   default_title
	Title	: default_title
	Usage	: $self->default_title($result)
	Function: Provides HTML	for the	given BLAST report that	will appear
		  at the top of	the BLAST report output.
	Returns	: empty	for text implementation
	Args	: First	argument is a Bio::Search::Result::ResultI

   introduction
	Title	: introduction
	Usage	: $self->introduction($CODE)

	 Function: Stores or returns the code to provide HTML for the given
		   BLAST report	detailing the query and	the
		   database information.
		   Useful for (for instance) specifying
		   routines returning alternative introductions.
		   Returns \&default_introduction (see below) if not
		   set.
	 Example : $index->introduction( \&my_introduction )
	 Returns : ref to CODE if called without arguments
	 Args	 : CODE

   default_introduction
	Title	: default_introduction
	Usage	: $self->default_introduction($result)
	Function: Outputs HTML to provide the query
		  and the database information
	Returns	: string containing HTML
	Args	: First	argument is a Bio::Search::Result::ResultI
		  Second argument is string holding literature citation

   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 (</BODY></HTML>)
		  for HTML
	Returns	: string
	Args	: none

   id_parser
	 Title	 : id_parser
	 Usage	 : $index->id_parser( CODE )
	 Function: Stores or returns the code used by record_id	to
		   parse the ID	for record from	a string.  Useful
		   for (for instance) specifying a different
		   parser for different	flavours of FASTA file.
		   Returns \&default_id_parser (see below) if not
		   set.	If you supply your own id_parser
		   subroutine, then it should expect a fasta
		   description line.  An entry will be added to
		   the index for each string in	the list returned.
	 Example : $index->id_parser( \&my_id_parser )
	 Returns : ref to CODE if called without arguments
	 Args	 : CODE

   default_id_parser
	 Title	 : default_id_parser
	 Usage	 : $id = default_id_parser( $header )
	 Function: The default Fasta ID	parser for Fasta.pm
		   Returns $1 from applying the	regexp /^>\s*(\S+)/
		   to $header.
	 Returns : ID string
	 Args	 : a fasta header line string

   algorithm_reference
	Title	: algorithm_reference
	Usage	: my $reference	= $writer->algorithm_reference($result);
	Function: Returns the appropriate Bibliographic	reference for the
		  algorithm format being produced
	Returns	: String
	Args	: L<Bio::Search::Result::ResultI> to reference

   Methods Bio::SearchIO::SearchWriterI
       Bio::SearchIO::SearchWriterI inherited methods.

   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

   no_wublastlinks
	Title	: no_wublastlinks
	Usage	: $obj->no_wublastlinks($newval)
	Function: Get/Set boolean value	regarding whether or not to display
		  Link = (1)
		  type output in the report output (WU-BLAST only)
	Returns	: boolean
	Args	: on set, new boolean value (a scalar or undef,	optional)

perl v5.24.1			  20Bio::SearchIO::Writer::TextResultWriter(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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