bio::searchio::writer::gbrowsegff(3pm) [debian man page]
Bio::SearchIO::Writer::GbrowseGFF(3pm) User Contributed Perl Documentation Bio::SearchIO::Writer::GbrowseGFF(3pm) NAME
Bio::SearchIO::Writer::GbrowseGFF - Interface for outputting parsed search results in Gbrowse GFF format SYNOPSIS
use Bio::SearchIO; my $in = Bio::SearchIO->new(-file => 'result.blast', -format => 'blast'); my $out = Bio::SearchIO->new(-output_format => 'GbrowseGFF', -output_cigar => 1, -output_signif => 1, -file => ">result.gff"); while( my $r = $in->next_result ) { $out->write_result($r); } DESCRIPTION
This writer produces Gbrowse flavour GFF from a Search::Result object. AUTHOR
Mark Wilkinson Email markw-at-illuminae-dot-com CONTRIBUTORS
Susan Miller sjmiller at email-DOT-arizon-DOT-edu Jason Stajich jason at bioperl-dot-org 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/ 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::Writer::GbrowseGFF->new(@args); Function: Builds a new Bio::SearchIO::Writer::GbrowseGFF object Returns : an instance of Bio::SearchIO::Writer::GbrowseGFF Args : -e_value => 10 : set e_value parsing cutoff (default undef) (note the -e_value flag is deprecated.) to_string Purpose : Produce the Gbrowse format GFF lines for a Result Usage : print $writer->to_string( $result_obj, @args); Argument : $result_obj = A Bio::Search::Result::ResultI object -version => 1|2|2.5|3 ; the GFF format you want to output (default 3) -match_tag => match|cDNA_match|EST_match|translated_nucleotide_match nucleotide_to_protein_match|nucleotide_motif This is the SO term to be placed in GFF column 3. -prefix => String to prefix the group by, default is EST (see %Defaults class variable) A default can also be set on object init Returns : String containing data for each search Result or any of its : sub-objects (Hits and HSPs). Throws : n/a start_report Title : start_report Usage : $self->start_report() Function: has no function, returns nothing Returns : empty string Args : none end_report Title : end_report Usage : $self->end_report() Function: has no function, returns nothing Returns : empty string Args : none filter Title : filter Usage : $writer->filter('hsp', &hsp_filter); Function: Filter out either at HSP,Hit,or Result level Returns : none Args : string => data type, CODE reference Note : GbrowseGFF.pm makes no changes to the default filter code perl v5.14.2 2012-03-02 Bio::SearchIO::Writer::GbrowseGFF(3pm)
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Bio::SearchIO::SearchResultEventBuilder(3pm) User Contributed Perl Documentation Bio::SearchIO::SearchResultEventBuilder(3pm) NAME
Bio::SearchIO::SearchResultEventBuilder - Event Handler for SearchIO events. SYNOPSIS
# Do not use this object directly, this object is part of the SearchIO # event based parsing system. DESCRIPTION
This object handles Search Events generated by the SearchIO classes and build appropriate Bio::Search::* objects from them. 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 CONTRIBUTORS
Sendu Bala, bix@sendu.me.uk 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::SearchResultEventBuilder->new(); Function: Builds a new Bio::SearchIO::SearchResultEventBuilder object Returns : Bio::SearchIO::SearchResultEventBuilder Args : -hsp_factory => Bio::Factory::ObjectFactoryI -hit_factory => Bio::Factory::ObjectFactoryI -result_factory => Bio::Factory::ObjectFactoryI See Bio::Factory::ObjectFactoryI for more information will_handle Title : will_handle Usage : if( $handler->will_handle($event_type) ) { ... } Function: Tests if this event builder knows how to process a specific event Returns : boolean Args : event type name SAX methods start_result Title : start_result Usage : $handler->start_result($resulttype) Function: Begins a result event cycle Returns : none Args : Type of Report end_result Title : end_result Usage : my @results = $parser->end_result Function: Finishes a result handler cycle Returns : A Bio::Search::Result::ResultI Args : none start_hsp Title : start_hsp Usage : $handler->start_hsp($name,$data) Function: Begins processing a HSP event Returns : none Args : type of element associated data (hashref) end_hsp Title : end_hsp Usage : $handler->end_hsp() Function: Finish processing a HSP event Returns : none Args : type of event and associated hashref start_hit Title : start_hit Usage : $handler->start_hit() Function: Starts a Hit event cycle Returns : none Args : type of event and associated hashref end_hit Title : end_hit Usage : $handler->end_hit() Function: Ends a Hit event cycle Returns : Bio::Search::Hit::HitI object Args : type of event and associated hashref Factory methods register_factory Title : register_factory Usage : $handler->register_factory('TYPE',$factory); Function: Register a specific factory for a object type class Returns : none Args : string representing the class and Bio::Factory::ObjectFactoryI See Bio::Factory::ObjectFactoryI for more information factory Title : factory Usage : my $f = $handler->factory('TYPE'); Function: Retrieves the associated factory for requested 'TYPE' Returns : a Bio::Factory::ObjectFactoryI Throws : Bio::Root::BadParameter if none registered for the supplied type Args : name of factory class to retrieve See Bio::Factory::ObjectFactoryI for more information inclusion_threshold See Bio::SearchIO::blast::inclusion_threshold. perl v5.14.2 2012-03-02 Bio::SearchIO::SearchResultEventBuilder(3pm)