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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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 [email protected]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)