| Bio::SearchIO::Writer::GbrowseGFF(3pm) | User Contributed Perl Documentation | Bio::SearchIO::Writer::GbrowseGFF(3pm) |
Bio::SearchIO::Writer::GbrowseGFF - Interface for outputting parsed search results in Gbrowse GFF format
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);
}
This writer produces Gbrowse flavour GFF from a Search::Result object.
Email markw-at-illuminae-dot-com
Susan Miller sjmiller at email-DOT-arizon-DOT-edu Jason Stajich jason at bioperl-dot-org
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.
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Please direct usage questions or support issues to the mailing list:
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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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.)
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
Title : start_report Usage : $self->start_report() Function: has no function, returns nothing Returns : empty string Args : none
Title : end_report Usage : $self->end_report() Function: has no function, returns nothing Returns : empty string Args : none
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
| 2021-08-15 | perl v5.32.1 |