Raw content of Bio::SearchIO # $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__