Reference

Bio::SearchIO::Writer::GbrowseGFF(3pm)

Interface for outputting parsed search results in Gbrowse GFF format

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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

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