Ewan Birney

NAME

Bio::SearchIO - Driver for parsing Sequence Database Searches (Blast,FASTA,...)

SYNOPSIS

    use Bio::SearchIO;
    my $searchio = new Bio::SearchIO( -format => 'blastxml',
                                      -file   => 'blastout.xml' );
    while ( my $result = $in->next_result() ) {
       while( my $hit = $result->next_hit ) {
        # process the Bio::Search::HitI object
           while( my $align = $sbjct->next_align ) { 
            # process the Bio::Search::HSPI object
        }
    }

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 Bio::Search::Result::ResultI compliant object, which is an object that represents one Blast/Fasta/HMMER whatever report.

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.

  bioperl-l@bioperl.org              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

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://bioperl.org/bioperl-bugs/

AUTHOR - Jason Stajich & Steve Chervitz

Email jason@bioperl.org Email sac@bioperl.org

CONTRIBUTORS

Additional contributors names and emails here

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 = 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

See Bio::Factory::ResultFactoryI, Bio::Factory::HitFactoryI, Bio::SearchIO::SearchWriterI

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    :

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    :

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 Bio::SearchIO::EventHandlerI

_eventHandler

 Title   : _eventHandler
 Usage   : private
 Function: Get the EventHandler
 Returns : Bio::SearchIO::EventHandlerI
 Args    : none

See Bio::SearchIO::EventHandlerI

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 Bio::Root::RootI

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 Bio::Root::Exception

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.

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 Bio::Factory::HitFactoryI

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 Bio::Factory::ResultFactoryI

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 Bio::Search::Hit::HitI

_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    :

_guess_format

 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function:
 Example :
 Returns : guessed format of filename (lower case)
 Args    :