bio::searchio::xml::blasthandler(3pm) [debian man page]
Bio::SearchIO::XML::BlastHandler(3pm) User Contributed Perl Documentation Bio::SearchIO::XML::BlastHandler(3pm) NAME
Bio::SearchIO::XML::BlastHandler - XML Handler for NCBI Blast XML parsing. SYNOPSIS
# This is not to be used directly. DESCRIPTION
This is the XML handler for BLAST XML parsing. Currently it passes elements off to the event handler, which is ultimately responsible for Bio::Search object generation. This was recently split off from the original code for Bio::SearchIO::blastxml primarily for maintenance purposes. DEPENDENCIES
In addition to parts of the Bio:: hierarchy, this module uses: XML::SAX::Base which comes with the XML::SAX distribution. FEEDBACK
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/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. 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 the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich, Chris Fields Email jason-at-bioperl.org Email cjfields-at-uiuc dot edu APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 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' perl v5.14.2 2012-03-02 Bio::SearchIO::XML::BlastHandler(3pm)
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Bio::SearchIO::axt(3pm) User Contributed Perl Documentation Bio::SearchIO::axt(3pm) NAME
Bio::SearchIO::axt - a parser for axt format reports SYNOPSIS
use Bio::SearchIO; my $parser = Bio::SearchIO->new(-format => 'axt', -file => 't/data/report.blastz'); while( my $result = $parser->next_result ) { while( my $hit = $result->next_hit ) { while( my $hsp = $hit->next_hsp ) { } } } DESCRIPTION
This is a parser and event-generator for AXT format reports. BLASTZ reports (Schwartz et al,(2003) Genome Research, 13:103-107) are normally in LAV format but are commonly post-processed to AXT format; many precomputed BLASTZ reports, such as those found in the UCSC Genome Browser, are in AXT format. This parser will also parse any AXT format produced from any lav report and directly out of BLAT. FEEDBACK
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/wiki/Mailing_lists - About the mailing lists Support Please direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. 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 the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Jason Stajich Email jason-at-bioperl.org APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $obj = Bio::SearchIO::axt->new(); Function: Builds a new Bio::SearchIO::axt object Returns : an instance of Bio::SearchIO::axt Args : 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 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 perl v5.14.2 2012-03-02 Bio::SearchIO::axt(3pm)