SYNOPSIS
use Bio::SearchIO;
use Bio::SearchIO::Writer::HTMLResultWriter;
my $in = Bio::SearchIO->new(-format => 'blast',
-file => shift @ARGV);
my $writer = Bio::SearchIO::Writer::HTMLResultWriter->new();
my $out = Bio::SearchIO->new(-writer => $writer);
$out->write_result($in->next_result);
# to filter your output
my $MinLength = 100; # need a variable with scope outside the method
sub hsp_filter {
my $hsp = shift;
return 1 if $hsp->length('total') > $MinLength;
}
sub result_filter {
my $result = shift;
return $hsp->num_hits > 0;
}
my $writer = Bio::SearchIO::Writer::HTMLResultWriter->new
(-filters => { 'HSP' => \&hsp_filter} );
my $out = Bio::SearchIO->new(-writer => $writer);
$out->write_result($in->next_result);
# can also set the filter via the writer object
$writer->filter('RESULT', \&result_filter);
DESCRIPTION
This object implements the SearchWriterI interface which will produce a set of HTML for a specific Bio::Search::Report::ReportI interface.See Bio::SearchIO::SearchWriterI for more info on the filter method.
FEEDBACK
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Reporting Bugs
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AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-orgCONTRIBUTORS
Gary Williams [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::HTMLResultWriter->new();
Function: Builds a new Bio::SearchIO::Writer::HTMLResultWriter object
Returns : Bio::SearchIO::Writer::HTMLResultWriter
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
-nucleotide_url => URL sprintf string base for the nt sequences
-protein_url => URL sprintf string base for the aa sequences
-no_wublastlinks => boolean. Do not display WU-BLAST lines
even if they are parsed out.
Links = (1)
remote_database_url
Title : remote_database_url
Usage : $obj->remote_database_url($type,$newval)
Function: This should return or set a string that contains a %s which can be
filled in with sprintf.
Returns : value of remote_database_url
Args : $type - 'PROTEIN' or 'P' for protein URLS
'NUCLEOTIDE' or 'N' for nucleotide URLS
$value - new value to set [optional]
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
hit_link_desc
Title : hit_link_desc
Usage : $self->hit_link_desc(\&link_function);
Function: Get/Set the function which provides an HTML
link(s) for the given hit to be used
within the description section at the top of the BLAST report.
This allows a person reading the report within
a web browser to go to one or more database entries for
the given hit from the description section.
Returns : Function reference
Args : Function reference
See Also: L<default_hit_link_desc()>
default_hit_link_desc
Title : default_hit_link_desc
Usage : $self->default_hit_link_desc($hit, $result)
Function: Provides an HTML link(s) for the given hit to be used
within the description section at the top of the BLAST report.
This allows a person reading the report within
a web browser to go to one or more database entries for
the given hit from the description section.
Returns : string containing HTML markup "<a href...")
The default implementation returns an HTML link to the
URL supplied by the remote_database_url() method
and using the identifier supplied by the id_parser() method.
It will use the NCBI GI if present, and the accession if not.
Args : First argument is a Bio::Search::Hit::HitI
Second argument is a Bio::Search::Result::ResultI
See Also: hit_link_align, remote_database, id_parser
hit_link_align
Title : hit_link_align
Usage : $self->hit_link_align(\&link_function);
Function: Get/Set the function which provides an HTML link(s)
for the given hit to be used
within the HSP alignment section of the BLAST report.
This allows a person reading the report within
a web browser to go to one or more database entries for
the given hit from the alignment section.
Returns : string containing HTML markup "<a href...")
The default implementation delegates to hit_link_desc().
Args : First argument is a Bio::Search::Hit::HitI
Second argument is a Bio::Search::Result::ResultI
See Also: hit_link_desc, remote_database, id_parser
hit_desc_line
Title : hit_desc_line
Usage : $self->hit_desc_line(\&link_function);
Function: Get/Set the function which provides HTML for the description
information from a hit. This allows one to parse
the rest of the description and split up lines, add links, etc.
Returns : Function reference
Args : Function reference
See Also: L<default_hit_link_desc()>
default_hit_desc_line
Title : default_hit_desc_line
Usage : $self->default_hit_desc_line($hit, $result)
Function: Parses the description line information, splits based on the
hidden \x01 between independent descriptions, checks the lines for
possible web links, and adds HTML link(s) for the given hit to be
used.
Returns : string containing HTML markup "<a href...")
The default implementation returns an HTML link to the
URL supplied by the remote_database_url() method
and using the identifier supplied by the id_parser() method.
It will use the NCBI GI if present, and the accession if not.
Args : First argument is a Bio::Search::Hit::HitI
Second argument is a Bio::Search::Result::ResultI
See Also: hit_link_align, remote_database, id_parser
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 HTML output.
Returns : string containing HTML markup
The default implementation returns <CENTER> <H1> HTML
containing text such as:
"Bioperl Reformatted HTML of BLASTP Search Report
for gi|1786183|gb|AAC73113.1|"
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
The default implementation checks for NCBI-style
identifiers in the given string ('gi|12345|AA54321').
For these IDs, it extracts the GI and accession and
returns a two-element list of strings (GI, acc).
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)