Bio::SearchIO::blasttable(3pm) | User Contributed Perl Documentation | Bio::SearchIO::blasttable(3pm) |
Bio::SearchIO::blasttable - Driver module for SearchIO for parsing NCBI -m 8/9 format
# do not use this module directly use Bio::SearchIO; my $parser = Bio::SearchIO->new(-file => $file, -format => 'blasttable'); while( my $result = $parser->next_result ) { }
This module will support parsing NCBI -m 8 or -m 9 tabular output and WU-BLAST -mformat 2 or -mformat 3 tabular output.
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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::blasttable->new(); Function: Builds a new Bio::SearchIO::blasttable object Returns : an instance of Bio::SearchIO::blasttable Args :
Title : next_result Usage : my $result = $parser->next_result Function: Parse the next result from the data stream Returns : L<Bio::Search::Result::ResultI> Args : none
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
Title : program_name Usage : $obj->program_name($newval) Function: Get/Set the program name Returns : value of program_name (a scalar) Args : on set, new value (a scalar or undef, optional)
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:
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().
2021-08-15 | perl v5.32.1 |