Bio::SearchIO::fasta - A SearchIO parser for FASTA results
# Do not use this object directly, use it through the SearchIO system use Bio::SearchIO; my $searchio = new Bio::SearchIO(-format => 'fasta', -file => 'report.FASTA'); while( my $result = $searchio->next_result ) { # .... }
This object contains the event based parsing code for FASTA format reports.
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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 = new Bio::SearchIO::fasta(); Function: Builds a new Bio::SearchIO::fasta object Returns : Bio::SearchIO::fasta Args : -idlength - set ID length to something other than the default (7), this is only necessary if you have compiled FASTA with a new default id length to display in the HSP alignment blocks
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 : 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 : idlength Usage : $obj->idlength($newval) Function: Internal storage of the length of the ID desc in the HSP alignment blocks. Defaults to $IDLENGTH class variable value Returns : value of idlength Args : newvalue (optional)
Title : result_count Usage : my $count = $searchio->result_count Function: Returns the number of results we have processed Returns : integer Args : none
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.