Bio::SearchIO::blastxml - A SearchIO implementation of NCBI Blast XML parsing. use Bio::SearchIO; my $searchin = new Bio::SearchIO(-format => 'blastxml', -file => 't/data/plague_yeast.bls.xml'); while( my $result = $searchin->next_result ) { } # one can also request that the parser NOT keep the XML data in memory # by using the tempfile initialization flag. my $searchin = new Bio::SearchIO(-tempfile => 1, -format => 'blastxml', -file => 't/data/plague_yeast.bls.xml'); while( my $result = $searchin->next_result ) { } This object implements a NCBI Blast XML parser. There is one additional initialization flag from the SearchIO defaults - that is the -tempfile flag. If specified as true, then the parser will write out each report to a temporary filehandle rather than holding the entire report as a string in memory. The reason this is done in the first place is NCBI reports have an uncessary <?xml version="1.0"?> at the beginning of each report and RPS-BLAST reports have an additional unecessary RPS-BLAST tag at the top of each report. So we currently have implemented the work around by preparsing the file (yes it makes the process slower, but it works).

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@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 $searchio = new Bio::SearchIO(-format => 'blastxml', -file => 'filename', -tempfile => 1); Function: Initializes the object - this is chained through new in SearchIO Returns : Bio::SearchIO::blastxml object Args : One additional argument from the format and file/fh parameters. -tempfile => boolean. Defaults to false. Write out XML data to a temporary filehandle to send to PerlSAX parser. =cut

_initialize
Title : _initialize Usage : private Function: Initializes the object - this is chained through new in SearchIO

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

SAX methods

start_document
Title : start_document Usage : $parser->start_document; Function: SAX method to indicate starting to parse a new document Returns : none Args : none

end_document
Title : end_document Usage : $parser->end_document; Function: SAX method to indicate finishing parsing a new document Returns : Bio::Search::Result::ResultI object Args : none

start_element
Title : start_element Usage : $parser->start_element($data) Function: SAX method to indicate starting a new element Returns : none Args : hash ref for data

end_element
Title : end_element Usage : $parser->end_element($data) Function: Signals finishing an element Returns : Bio::Search object dpending on what type of element Args : hash ref for data

characters
Title : characters Usage : $parser->characters($data) Function: Signals new characters to be processed Returns : characters read Args : hash ref with the key 'Data'

use_tempfile
Title : use_tempfile Usage : $obj->use_tempfile($newval) Function: Get/Set boolean flag on whether or not use a tempfile Example : Returns : value of use_tempfile Args : newvalue (optional)