Bio::SearchIO - Driver for parsing Sequence Database Searches (Blast,FASTA,...)
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
}
}
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 Bio::Search::Result::ResultI compliant object, which is an object that represents one Blast/Fasta/HMMER whatever report.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 Bio::Factory::ResultFactoryI, Bio::Factory::HitFactoryI, Bio::SearchIO::SearchWriterI
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 :
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 :
Title : attach_EventHandler Usage : $parser->attatch_EventHandler($handler) Function: Adds an event handler to listen for events Returns : none Args : Bio::SearchIO::EventHandlerI
See Bio::SearchIO::EventHandlerI
Title : _eventHandler Usage : private Function: Get the EventHandler Returns : Bio::SearchIO::EventHandlerI Args : none
See Bio::SearchIO::EventHandlerI
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 Bio::Root::RootI
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.
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.
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.
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 Bio::Factory::ResultFactoryI
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
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
Title : _load_format_module Usage : *INTERNAL SearchIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args :
