From Code to Community: Sponsoring The Perl and Raku Conference 2025 Learn more

 / 
BioPerl-1.7.8
River stage two • 60 direct dependents • 64 total dependents
/ Bio::SearchIO::blast

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

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)