bio::searchio::searchwriteri(3pm) [debian man page]
Bio::SearchIO::SearchWriterI(3pm) User Contributed Perl Documentation Bio::SearchIO::SearchWriterI(3pm) NAME
Bio::SearchIO::SearchWriterI - Interface for outputting parsed Search results SYNOPSIS
Bio::SearchIO::SearchWriterI objects cannot be instantiated since this module defines a pure interface. Given an object that implements the Bio::SearchIO::SearchWriterI interface, you can do the following things with it: print $writer->to_string( $result_obj, @args ); DESCRIPTION
This module defines abstract methods that all subclasses must implement to be used for outputting results from Bio::Search::Result::ResultI objects. AUTHOR
Steve Chervitz <sac-at-bioperl.org> DISCLAIMER
This software is provided "as is" without warranty of any kind. APPENDIX
The rest of the documentation details each of the object methods. to_string Purpose : Produces data for each Search::Result::ResultI in a string. : This is an abstract method. For some useful implementations, : see ResultTableWriter.pm, HitTableWriter.pm, : and HSPTableWriter.pm. Usage : print $writer->to_string( $result_obj, @args ); Argument : $result_obj = A Bio::Search::Result::ResultI object : @args = any additional arguments used by your implementation. 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: The method to call when starting a report. You can override it to make a custom header Returns : string Args : none end_report Title : end_report Usage : $self->end_report() Function: The method to call when ending a report, this is mostly for cleanup for formats which require you to have something at the end of the document (</BODY></HTML>) for HTML Returns : 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 perl v5.14.2 2012-03-02 Bio::SearchIO::SearchWriterI(3pm)
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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)