Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::SearchIO::blast - Event generator for event based parsing of blast reports

SYNOPSIS

          # Do not use this object directly - it is used as part of the
          # Bio::SearchIO system.

           use Bio::SearchIO;
           my $searchio = Bio::SearchIO->new(-format => 'blast',
                                            -file   => 't/data/ecolitst.bls');
           while( my $result = $searchio->next_result ) {
               while( my $hit = $result->next_hit ) {
                   while( my $hsp = $hit->next_hsp ) {
                       # ...
                   }
               }
           }

DESCRIPTION

       This object encapsulated the necessary methods for generating events suitable for building
       Bio::Search objects from a BLAST report file.  Read the Bio::SearchIO for more information
       about how to use this.

       This driver can parse:

       ·   NCBI produced plain text BLAST reports from blastall, this also includes PSIBLAST,
           PSITBLASTN, RPSBLAST, and bl2seq reports.  NCBI XML BLAST output is parsed with the
           blastxml SearchIO driver

       ·   WU-BLAST all reports

       ·   Jim Kent's BLAST-like output from his programs (BLASTZ, BLAT)

       ·   BLAST-like output from Paracel BTK output

   bl2seq parsing
       Since I cannot differentiate between BLASTX and TBLASTN since bl2seq doesn't report the
       algorithm used - I assume it is BLASTX by default - you can supply the program type with
       -report_type in the SearchIO constructor i.e.

         my $parser = Bio::SearchIO->new(-format => 'blast',
                                        -file => 'bl2seq.tblastn.report',
                                        -report_type => 'tblastn');

       This only really affects where the frame and strand information are put - they will always
       be on the $hsp->query instead of on the $hsp->hit part of the feature pair for blastx and
       tblastn bl2seq produced reports.  Hope that's clear...

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

       Email Jason Stajich jason-at-bioperl.org

CONTRIBUTORS

       Steve Chervitz 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::blast->new(%args);
        Function: Builds a new Bio::SearchIO::blast object
        Returns : Bio::SearchIO::blast
        Args    : Key-value pairs:
                  -fh/-file => filehandle/filename to BLAST file
                  -format   => 'blast'
                  -report_type => 'blastx', 'tblastn', etc -- only for bl2seq
                                  reports when you want to distinguish between
                                  tblastn and blastx reports (this only controls
                                  where the frame information is put - on the query
                                  or subject object.
                  -inclusion_threshold => e-value threshold for inclusion in the
                                          PSI-BLAST score matrix model (blastpgp)
                  -signif      => float or scientific notation number to be used
                                  as a P- or Expect value cutoff
                  -score       => integer or scientific notation number to be used
                                  as a blast score value cutoff
                  -bits        => integer or scientific notation number to be used
                                  as a bit score value cutoff
                  -hit_filter  => reference to a function to be used for
                                  filtering hits based on arbitrary criteria.
                                  All hits of each BLAST report must satisfy
                                  this criteria to be retained.
                                  If a hit fails this test, it is ignored.
                                  This function should take a
                                  Bio::Search::Hit::BlastHit.pm object as its first
                                  argument and return true
                                  if the hit should be retained.
                                  Sample filter function:
                                     -hit_filter => sub { $hit = shift;
                                                          $hit->gaps == 0; },
                                  (Note: -filt_func is synonymous with -hit_filter)
                  -overlap     => integer. The amount of overlap to permit between
                                  adjacent HSPs when tiling HSPs. A reasonable value is 2.
                                  Default = $Bio::SearchIO::blast::MAX_HSP_OVERLAP.

                   The following criteria are not yet supported:
                   (these are probably best applied within this module rather than in the
                    event handler since they would permit the parser to take some shortcuts.)

                  -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.

   next_result
        Title   : next_result
        Usage   : my $hit = $searchio->next_result;
        Function: Returns the next Result from a search
        Returns : Bio::Search::Result::ResultI object
        Args    : none

   _will_handle
        Title   : _will_handle
        Usage   : Private method. For internal use only.
                     if( $self->_will_handle($type) ) { ... }
        Function: Provides an optimized way to check whether or not an element of a
                  given type is to be handled.
        Returns : Reference to EventHandler object if the element type is to be handled.
                  undef if the element type is not to be handled.
        Args    : string containing type of element.

       Optimizations:

       1.
         Using the cached pointer to the EventHandler to minimize repeated lookups.

       2.
         Caching the will_handle status for each type that is encountered so that it only need be
         checked by calling handler->will_handle($type) once.

       This does not lead to a major savings by itself (only 5-10%).  In combination with other
       optimizations, or for large parse jobs, the savings good be significant.

       To test against the unoptimized version, remove the parentheses from around the third term
       in the ternary " ? : " operator and add two calls to $self->_eventHandler().

   start_element
        Title   : start_element
        Usage   : $eventgenerator->start_element
        Function: Handles a start element event
        Returns : none
        Args    : hashref with at least 2 keys 'Data' and 'Name'

   end_element
        Title   : end_element
        Usage   : $eventgenerator->end_element
        Function: Handles an end element event
        Returns : hashref with an element's worth of data
        Args    : hashref with at least 2 keys 'Data' and 'Name'

   element
        Title   : element
        Usage   : $eventhandler->element({'Name' => $name, 'Data' => $str});
        Function: Convenience method that calls start_element, characters, end_element
        Returns : none
        Args    : Hash ref with the keys 'Name' and 'Data'

   characters
        Title   : characters
        Usage   : $eventgenerator->characters($str)
        Function: Send a character events
        Returns : none
        Args    : string

   within_element
        Title   : within_element
        Usage   : if( $eventgenerator->within_element($element) ) {}
        Function: Test if we are within a particular element
                  This is different than 'in' because within can be tested
                  for a whole block.
        Returns : boolean
        Args    : string element name

       See Also: in_element

   in_element
        Title   : in_element
        Usage   : if( $eventgenerator->in_element($element) ) {}
        Function: Test if we are in a particular element
                  This is different than 'within_element' because within
                  can be tested for a whole block.
        Returns : boolean
        Args    : string element name

       See Also: within_element

   start_document
        Title   : start_document
        Usage   : $eventgenerator->start_document
        Function: Handle a start document event
        Returns : none
        Args    : none

   end_document
        Title   : end_document
        Usage   : $eventgenerator->end_document
        Function: Handles an end document event
        Returns : Bio::Search::Result::ResultI object
        Args    : 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)