Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

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

SYNOPSIS

          use Bio::SearchIO;
          # format can be 'fasta', 'blast', 'exonerate', ...
          my $searchio = Bio::SearchIO->new( -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 (both NCBI and WUBLAST tabular)
         megablast  MEGABLAST
         psl        UCSC PSL format
         waba       WABA output
         axt        AXT format
         sim4       Sim4
         hmmer      HMMER2 hmmpfam and hmmsearch or HMMER3 hmmscan and hmmsearch
         exonerate  Exonerate CIGAR and VULGAR format
         blastxml   NCBI BLAST XML
         wise       Genewise -genesf format

       Also see the SearchIO HOWTO: http://bioperl.org/howtos/SearchIO_HOWTO.html

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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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:

         https://github.com/bioperl/bioperl-live/issues

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 = Bio::SearchIO->new();
        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
                  -inclusion_threshold => e-value threshold for inclusion in the
                                          PSI-BLAST score matrix model
                  -signif         => float or scientific notation number to be used
                                     as a P- or Expect value cutoff
                  -check_all_hits => boolean. Check all hits for significance against
                                     significance criteria.  Default = false.
                                     If false, stops processing hits after the first
                                     non-significant hit or the first hit that fails
                                     the hit_filter call. This speeds parsing,
                                     taking advantage of the fact that the hits are
                                     processed in the order they appear in the report.
                  -min_query_len  => integer to be used as a minimum for query sequence
                                     length. Reports with query sequences below this
                                     length will not be processed.
                                     default = no minimum length.
                  -best           => boolean. Only process the best hit of each report;
                                     default = false.

       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    :

   format
        Title   : format
        Usage   : $format = $obj->format()
        Function: Get the search format
        Returns : search format
        Args    : none

   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

   write_report
        Title   : write_report
        Usage   : $stream->write_report(SearchIO stream, @other_args)
        Function: Writes data directly from the SearchIO stream object into the
                : writer.  This is mainly useful if one has multiple ResultI objects
                : in a SearchIO stream and you don't want to reiterate header/footer
                : between each call.
        Returns : 1 for success and 0 for error
        Args    : Bio::SearchIO stream 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 successfully parsed
                  at the point of the method call.  This is not the total # of results
                  in the file.
        Returns : integer
        Args    : none
        Throws  : none

   inclusion_threshold
        Title   : inclusion_threshold
        Usage   : my $incl_thresh = $isreb->inclusion_threshold;
                : $isreb->inclusion_threshold(1e-5);
        Function: Get/Set the e-value threshold for inclusion in the PSI-BLAST
                  score matrix model (blastpgp) that was used for generating the reports
                  being parsed.
        Returns : number (real)
                  Default value: $Bio::SearchIO::IteratedSearchResultEventBuilder::DEFAULT_INCLUSION_THRESHOLD
        Args    : number (real)  (e.g., 0.0001 or 1e-4 )

   max_significance
        Usage     : $obj->max_significance();
        Purpose   : Set/Get the P or Expect value used as significance screening cutoff.
                    This is the value of the -signif parameter supplied to new().
                    Hits with P or E-value above this are skipped.
        Returns   : Scientific notation number with this format: 1.0e-05.
        Argument  : Scientific notation number or float (when setting)
        Comments  : Screening of significant hits uses the data provided on the
                  : description line. For NCBI BLAST1 and WU-BLAST, this data
                  : is P-value. for NCBI BLAST2 it is an Expect value.

   signif
       Synonym for max_significance()

   min_score
        Usage     : $obj->min_score();
        Purpose   : Set/Get the Blast score used as screening cutoff.
                    This is the value of the -score parameter supplied to new().
                    Hits with scores below this are skipped.
        Returns   : Integer or scientific notation number.
        Argument  : Integer or scientific notation number (when setting)
        Comments  : Screening of significant hits uses the data provided on the
                  : description line.

   min_query_length
        Usage     : $obj->min_query_length();
        Purpose   : Gets the query sequence length used as screening criteria.
                    This is the value of the -min_query_len parameter supplied to new().
                    Hits with sequence length below this are skipped.
        Returns   : Integer
        Argument  : n/a

   best_hit_only
        Title     : best_hit_only
        Usage     : print "only getting best hit.\n" if $obj->best_hit_only;
        Purpose   : Set/Get the indicator for whether or not to process only
                  : the best BlastHit.
        Returns   : Boolean (1 | 0)
        Argument  : Boolean (1 | 0) (when setting)

   check_all_hits
        Title     : check_all_hits
        Usage     : print "checking all hits.\n" if $obj->check_all_hits;
        Purpose   : Set/Get the indicator for whether or not to process all hits.
                  : If false, the parser will stop processing hits after the
                  : the first non-significance hit or the first hit that fails
                  : any hit filter.
        Returns   : Boolean (1 | 0)
        Argument  : Boolean (1 | 0) (when setting)

   _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    :

   _get_seq_identifiers
        Title   : _get_seq_identifiers
        Usage   : my ($gi, $acc,$ver) = &_get_seq_identifiers($id)
        Function: Private function to get the gi, accession, version data
                  for an ID (if it is in NCBI format)
        Returns : 3-pule of gi, accession, version
        Args    : ID string to process (NCBI format)

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