Bio::SearchIO::blast.3pm

Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 3 (Bibliothèques de fonctions)

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

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)