Bio::SearchIO::megablast(3pm) | User Contributed Perl Documentation | Bio::SearchIO::megablast(3pm) |
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 = Bio::SearchIO->new(-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 # gap characters + # 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 + gap characters). 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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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : my $obj = Bio::SearchIO::blast->new(); Function: Builds a new Bio::SearchIO::blast object Returns : Bio::SearchIO::blast Args : -fh/-file => filehandle/filename to BLAST file -format => 'blast'
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
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)
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'
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'
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'
Title : characters Usage : $eventgenerator->characters($str) Function: Send a character events Returns : none Args : string
Title : _mode Usage : $obj->_mode($newval) Function: Example : Returns : value of _mode Args : newvalue (optional)
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
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
Title : start_document Usage : $eventgenerator->start_document Function: Handles a start document event Returns : none Args : none
Title : end_document Usage : $eventgenerator->end_document Function: Handles an end document event Returns : Bio::Search::Result::ResultI object Args : none
Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none
2018-10-27 | perl v5.26.2 |