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://github.com/bioperl/bioperl-live/issues

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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq