/ 
bioperl-1.5.2_004-RCf
/ Bio::SearchIO

NAME

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

SYNOPSIS

use Bio::SearchIO;
# format can be 'fasta', 'blast', 'exonerate', ...
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
        }
    }
}

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.

A list of module names and formats is below:

blast      BLAST (WUBLAST, NCBIBLAST,bl2seq)   
fasta      FASTA -m9 and -m0
blasttable BLAST -m9 or -m8 output (NCBI not WUBLAST tabular)
megablast  MEGABLAST
psl        UCSC PSL format
waba       WABA output
axt        AXT format
sim4       Sim4
hmmer      HMMER hmmpfam and hmmsearch
exonerate  Exonerate CIGAR and VULGAR format
blastxml   NCBI BLAST XML
wise       Genewise -genesf format

Also see the SearchIO HOWTO: http://bioperl.open-bio.org/wiki/HOWTO:SearchIO

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/wiki/Mailing_lists  - 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 the web:

http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich & Steve Chervitz

Email jason-at-bioperl.org Email sac-at-bioperl.org

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    : -file           => $filename
          -format         => format
          -fh             => filehandle to attach to
          -result_factory => Object implementing Bio::Factory::ObjectFactoryI
          -hit_factory    => Object implementing Bio::Factory::ObjectFactoryI
          -hsp_factory    => Object implementing Bio::Factory::ObjectFactoryI
          -writer         => Object implementing Bio::SearchIO::SearchWriterI
          -output_format  => output format, which will dynamically load writer

See Bio::Factory::ObjectFactoryI, Bio::SearchIO::SearchWriterI

Any factory objects in the arguments are passed along to the SearchResultEventBuilder object which holds these factories and sets default ones if none are supplied as arguments.

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.

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

_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    :