Raw content of Bio::SearchIO
<![CDATA[# $Id: SearchIO.pm,v 1.18 2002/12/13 13:54:03 jason Exp $
#
# BioPerl module for Bio::SearchIO
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SearchIO - Driver for parsing Sequence Database Searches (Blast,FASTA,...)
=head1 SYNOPSIS
use Bio::SearchIO;
# format can be 'fasta', 'blast'
my $searchio = new Bio::SearchIO( -format => 'blastxml',
-file => 'blastout.xml' );
while ( my $result = $searchio->next_result() ) {
while( my $hit = $result->next_hit ) {
# process the Bio::Search::Hit::HitI object
while( my $hsp = $hit->next_hsp ) {
# process the Bio::Search::HSP::HSPI object
}
}
=head1 DESCRIPTION
This is a driver for instantiating a parser for report files from
sequence database searches. This object serves as a wrapper for the
format parsers in Bio::SearchIO::* - you should not need to ever
use those format parsers directly. (For people used to the SeqIO
system it, we are deliberately using the same pattern).
Once you get a SearchIO object, calling next_result() gives you back
a L<Bio::Search::Result::ResultI> compliant object, which is an object that
represents one Blast/Fasta/HMMER whatever report.
=head1 FEEDBACK
=head2 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/MailList.shtml - About the mailing lists
=head2 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
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich & Steve Chervitz
Email jason@bioperl.org
Email sac@bioperl.org
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SearchIO;
use strict;
use vars qw(@ISA);
# Object preamble - inherits from Bio::Root::IO
use Bio::Root::IO;
use Bio::Event::EventGeneratorI;
use Bio::SearchIO::SearchResultEventBuilder;
use Bio::AnalysisParserI;
use Symbol();
@ISA = qw( Bio::Root::IO Bio::Event::EventGeneratorI Bio::AnalysisParserI);
=head2 new
Title : new
Usage : my $obj = new Bio::SearchIO();
Function: Builds a new Bio::SearchIO object
Returns : Bio::SearchIO initialized with the correct format
Args : Args : -file => $filename
-format => format
-fh => filehandle to attach to
-result_factory => Object implementing Bio::Factory::ResultFactoryI
-hit_factory => Object implementing Bio::Factory::HitFactoryI
-writer => Object implementing Bio::SearchIO::SearchWriterI
-output_format => output format, which will dynamically load writer
See L<Bio::Factory::ResultFactoryI>, L<Bio::Factory::HitFactoryI>,
L<Bio::SearchIO::SearchWriterI>
=cut
sub new {
my($caller,@args) = @_;
my $class = ref($caller) || $caller;
# or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::SearchIO::(\S+)/ ) {
my ($self) = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
} else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $format = $param{'-format'} ||
$class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'blast';
my $output_format = $param{'-output_format'};
my $writer = undef;
if( defined $output_format ) {
if( defined $param{'-writer'} ) {
my $dummy = Bio::Root::Root->new();
$dummy->throw("Both writer and output format specified - not good");
}
if( $output_format =~ /^blast$/i ) {
$output_format = 'TextResultWriter';
}
my $output_module = "Bio::SearchIO::Writer::".$output_format;
$class->_load_module($output_module);
$writer = $output_module->new();
push(@args,"-writer",$writer);
}
# normalize capitalization to lower case
$format = "\L$format";
return undef unless( $class->_load_format_module($format) );
return "Bio::SearchIO::${format}"->new(@args);
}
}
=head2 newFh
Title : newFh
Usage : $fh = Bio::SearchIO->newFh(-file=>$filename,
-format=>'Format')
Function: does a new() followed by an fh()
Example : $fh = Bio::SearchIO->newFh(-file=>$filename,
-format=>'Format')
$result = <$fh>; # read a ResultI object
print $fh $result; # write a ResultI object
Returns : filehandle tied to the Bio::SearchIO::Fh class
Args :
=cut
sub newFh {
my $class = shift;
return unless my $self = $class->new(@_);
return $self->fh;
}
=head2 fh
Title : fh
Usage : $obj->fh
Function:
Example : $fh = $obj->fh; # make a tied filehandle
$result = <$fh>; # read a ResultI object
print $fh $result; # write a ResultI object
Returns : filehandle tied to the Bio::SearchIO::Fh class
Args :
=cut
sub fh {
my $self = shift;
my $class = ref($self) || $self;
my $s = Symbol::gensym;
tie $$s,$class,$self;
return $s;
}
=head2 attach_EventHandler
Title : attach_EventHandler
Usage : $parser->attatch_EventHandler($handler)
Function: Adds an event handler to listen for events
Returns : none
Args : Bio::SearchIO::EventHandlerI
See L<Bio::SearchIO::EventHandlerI>
=cut
sub attach_EventHandler{
my ($self,$handler) = @_;
return if( ! $handler );
if( ! $handler->isa('Bio::SearchIO::EventHandlerI') ) {
$self->warn("Ignoring request to attatch handler ".ref($handler). ' because it is not a Bio::SearchIO::EventHandlerI');
}
$self->{'_handler'} = $handler;
return;
}
=head2 _eventHandler
Title : _eventHandler
Usage : private
Function: Get the EventHandler
Returns : Bio::SearchIO::EventHandlerI
Args : none
See L<Bio::SearchIO::EventHandlerI>
=cut
sub _eventHandler{
my ($self) = @_;
return $self->{'_handler'};
}
sub _initialize {
my($self, @args) = @_;
$self->{'_handler'} = undef;
# not really necessary unless we put more in RootI
#$self->SUPER::_initialize(@args);
# initialize the IO part
$self->_initialize_io(@args);
$self->attach_EventHandler(new Bio::SearchIO::SearchResultEventBuilder());
$self->{'_reporttype'} = '';
my ( $writer, $rfactory, $hfactory, $use_factories ) =
$self->_rearrange([qw(WRITER
RESULT_FACTORY
HIT_FACTORY
USE_FACTORIES)], @args);
$self->writer( $writer ) if $writer;
# TODO: Resolve this issue:
# The $use_factories flag is a temporary hack to allow factory-based and
# non-factory based SearchIO objects to co-exist.
# steve --- Sat Dec 22 04:41:20 2001
if( $use_factories) {
if( not defined $self->{'_result_factory'}) {
$self->result_factory( $rfactory || $self->default_result_factory_class->new );
}
if( not defined $self->{'_hit_factory'}) {
$self->hit_factory( $hfactory || $self->default_hit_factory_class->new );
}
}
}
=head2 next_result
Title : next_result
Usage : $result = stream->next_result
Function: Reads the next ResultI object from the stream and returns it.
Certain driver modules may encounter entries in the stream that
are either misformatted or that use syntax not yet understood
by the driver. If such an incident is recoverable, e.g., by
dismissing a feature of a feature table or some other non-mandatory
part of an entry, the driver will issue a warning. In the case
of a non-recoverable situation an exception will be thrown.
Do not assume that you can resume parsing the same stream after
catching the exception. Note that you can always turn recoverable
errors into exceptions by calling $stream->verbose(2) (see
Bio::Root::RootI POD page).
Returns : A Bio::Search::Result::ResultI object
Args : n/a
See L<Bio::Root::RootI>
=cut
sub next_result {
my ($self) = @_;
$self->throw_not_implemented;
}
=head2 write_result
Title : write_result
Usage : $stream->write_result($result_result, @other_args)
Function: Writes data from the $result_result object into the stream.
: Delegates to the to_string() method of the associated
: WriterI object.
Returns : 1 for success and 0 for error
Args : Bio::Search:Result::ResultI object,
: plus any other arguments for the Writer
Throws : Bio::Root::Exception if a Writer has not been set.
See L<Bio::Root::Exception>
=cut
sub write_result {
my ($self, $result, @args) = @_;
if( not ref($self->{'_result_writer'}) ) {
$self->throw("ResultWriter not defined.");
}
my $str = $self->writer->to_string( $result, @args );
#print "Got string: \n$str\n";
$self->_print( "$str" );
return 1;
}
=head2 writer
Title : writer
Usage : $writer = $stream->writer;
Function: Sets/Gets a SearchWriterI object to be used for this searchIO.
Returns : 1 for success and 0 for error
Args : Bio::SearchIO::SearchWriterI object (when setting)
Throws : Bio::Root::Exception if a non-Bio::SearchIO::SearchWriterI object
is passed in.
=cut
sub writer {
my ($self, $writer) = @_;
if( ref($writer) and $writer->isa( 'Bio::SearchIO::SearchWriterI' )) {
$self->{'_result_writer'} = $writer;
}
elsif( defined $writer ) {
$self->throw("Can't set ResultWriter. Not a Bio::SearchIO::SearchWriterI: $writer");
}
return $self->{'_result_writer'};
}
=head2 hit_factory
Title : hit_factory
Usage : $hit_factory = $stream->hit_factory; (get)
: $stream->hit_factory( $factory ); (set)
Function: Sets/Gets a factory object to create hit objects for this SearchIO
Returns : Bio::Factory::HitFactoryI object
Args : Bio::Factory::HitFactoryI object (when setting)
Throws : Bio::Root::Exception if a non-Bio::Factory::HitFactoryI object
is passed in.
Comments: A SearchIO implementation should provide a default hit factory.
See L<Bio::Factory::HitFactoryI>
=cut
sub hit_factory {
my ($self, $fact) = @_;
if( ref $fact and $fact->isa( 'Bio::Factory::HitFactoryI' )) {
$self->{'_hit_factory'} = $fact;
}
elsif( defined $fact ) {
$self->throw("Can't set HitFactory. Not a Bio::Factory::HitFactoryI: $fact");
}
return $self->{'_hit_factory'};
}
=head2 result_factory
Title : result_factory
Usage : $result_factory = $stream->result_factory; (get)
: $stream->result_factory( $factory ); (set)
Function: Sets/Gets a factory object to create result objects for this
SearchIO.
Returns : Bio::Factory::ResultFactoryI object
Args : Bio::Factory::ResultFactoryI object (when setting)
Throws : Bio::Root::Exception if a non-Bio::Factory::ResultFactoryI object
is passed in.
Comments: A SearchIO implementation should provide a default result factory.
See L<Bio::Factory::ResultFactoryI>
=cut
sub result_factory {
my ($self, $fact) = @_;
if( ref $fact and $fact->isa( 'Bio::Factory::ResultFactoryI' )) {
$self->{'_result_factory'} = $fact;
}
elsif( defined $fact ) {
$self->throw("Can't set ResultFactory. Not a Bio::Factory::ResultFactoryI: $fact");
}
return $self->{'_result_factory'};
}
=head2 result_count
Title : result_count
Usage : $num = $stream->result_count;
Function: Gets the number of Blast results that have been parsed.
Returns : integer
Args : none
Throws : none
=cut
sub result_count {
my $self = shift;
$self->throw_not_implemented;
}
=head2 default_hit_factory_class
Title : default_hit_factory_class
Usage : $res_factory = $obj->default_hit_factory_class()->new( @args )
Function: Returns the name of the default class to be used for creating
Bio::Search::Hit::HitI objects.
Example :
Returns : A string containing the name of a class that implements
the Bio::Search::Hit::HitI interface.
Args : none
Comments: Bio::SearchIO does not implement this method. It throws a
NotImplemented exception
See L<Bio::Search::Hit::HitI>
=cut
sub default_hit_factory_class {
my $self = shift;
# TODO: Uncomment this when Jason's SearchIO code conforms
# $self->throw_not_implemented;
}
=head2 _load_format_module
Title : _load_format_module
Usage : *INTERNAL SearchIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
=cut
sub _load_format_module {
my ($self,$format) = @_;
my $module = "Bio::SearchIO::" . $format;
my $ok;
eval {
$ok = $self->_load_module($module);
};
if ( $@ ) {
print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the SearchIO system please see the SearchIO docs.
This includes ways of checking for formats at compile time, not run time
END
;
}
return $ok;
}
=head2 _guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
=cut
sub _guess_format {
my $class = shift;
return unless $_ = shift;
return 'blast' if (/blast/i or /\.bl\w$/i);
return 'fasta' if (/fasta/i or /\.fas$/i);
return 'blastxml' if (/blast/i and /\.xml$/i);
return 'exonerate' if ( /\.exonerate/i or /\.exon/i );
}
sub close {
my $self = shift;
if( $self->writer ) {
$self->_print($self->writer->end_report());
}
$self->SUPER::close(@_);
}
sub DESTROY {
my $self = shift;
$self->close();
}
sub TIEHANDLE {
my $class = shift;
return bless {processor => shift}, $class;
}
sub READLINE {
my $self = shift;
return $self->{'processor'}->next_result() unless wantarray;
my (@list, $obj);
push @list, $obj while $obj = $self->{'processor'}->next_result();
return @list;
}
sub PRINT {
my $self = shift;
$self->{'processor'}->write_result(@_);
}
1;
__END__
]]>