Bio::SearchIO::blast - Event generator for event based parsing of blast reports # Do not use this object directly - it is used as part of the # Bio::SearchIO system. use Bio::SearchIO; my $searchio = new Bio::SearchIO(-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 ) { # ... } } } 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 = new Bio::SearchIO(-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...

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/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ Email Jason Stajich jason-at-bioperl.org Steve Chervitz sac-at-bioperl.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::SearchIO::blast(%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: Using the cached pointer to the EventHandler to minimize repeated lookups. 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 : start_element Usage : $eventgenerator->end_element Function: Handles an end element event Returns : none 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)

_get_accession_version
Title : _get_accession_version Usage : my ($acc,$ver) = &_get_accession_version($id) Function:Private function to get an accession,version pair for an ID (if it is in NCBI format) Returns : 2-pule of accession, version Args : ID string to process