Bio::SearchIO::megablast - a driver module for Bio::SearchIO to parse megablast reports (format 0) # do not use this module directly use Bio::SearchIO; # for default format output from megablast my $in = new Bio::SearchIO(-file => 'file.mbl', -format => 'megablast', -report_format => 0); while( my $r = $in->next_result ) { while( my $hit = $r->next_hit ) { while( my $hsp = $hit->next_hsp ) { } } } Beware! Because of the way megablast report format 0 is coded, realize that score means # gaps + # mismatches for a HSP. The docs from NCBI regarding FORMAT 0 # 0: Produce one-line output for each alignment, in the form # # 'subject-id'=='[+-]query-id' (s_off q_off s_end q_end) score # # Here subject(query)-id is a gi number, an accession or some other type of # identifier found in the FASTA definition line of the respective sequence. # # + or - corresponds to same or different strand alignment. # # Score for non-affine gapping parameters means the total number of # differences (mismatches + gaps). For affine case it is the actual (raw) # score of the alignment. FORMAT 1 parsing has not been implemented FORMAT 2 parsing should work with the SearchIO 'blast' parser

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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://bioperl.org/bioperl-bugs/ Email jason@bioperl.org Describe contact details here Additional contributors names and emails here 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(); Function: Builds a new Bio::SearchIO::blast object Returns : Bio::SearchIO::blast Args : -fh/-file => filehandle/filename to BLAST file -format => 'blast'

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

report_format
Title : report_format Usage : $obj->report_format($newval) Function: Get/Set the report_format value Returns : value of report_format (a scalar) Args : on set, new value (a scalar or undef, optional)

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: Convience 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

_mode
Title : _mode Usage : $obj->_mode($newval) Function: Example : Returns : value of _mode Args : newvalue (optional)

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

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

start_document
Title : start_document Usage : $eventgenerator->start_document Function: Handles 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

result_count
Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none