bl2seq parsing

  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...

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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

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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

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)