NAME

       Bio::FeatureIO::gff - read/write GFF feature files

SYNOPSIS

         my $feature; #get a Bio::SeqFeature::Annotated somehow
         my $featureOut = Bio::FeatureIO->new(
           -format => 'gff',
           -version => 3,
           -fh => \*STDOUT,
           -validate_terms => 1, #boolean. validate ontology terms online?  default 0 (false).
         );
         $featureOut->write_feature($feature);

DESCRIPTION

        Currently implemented:

        version         read?   write?
        ------------------------------
        GFF 1             N       N
        GFF 2             N       N
        GFF 2.5 (GTF)     N       Y
        GFF 3             Y       Y

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_list  - 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:

         http://bugzilla.open-bio.org/

AUTHOR

        Allen Day, <allenday@ucla.edu>

CONTRIBUTORS

        Steffen Grossmann, <grossman@molgen.mpg.de>
        Scott Cain, <cain@cshl.edu>
        Rob Edwards <rob@salmonella.org>

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   next_feature()
        Usage   : my $feature = $featureio->next_feature();
        Function: reads a feature record from a GFF stream and returns it as an object.
        Returns : a Bio::SeqFeature::Annotated object
        Args    : N/A

   next_feature_group
        Title   : next_feature_group
        Usage   : @feature_group = $stream->next_feature_group
        Function: Reads the next feature_group from $stream and returns it.

                  Feature groups in GFF3 files are separated by '###' directives. The
                  features in a group might form a hierarchical structure. The
                  complete hierarchy of features is returned, i.e. the returned array
                  represents only the top-level features.  Lower-level features can
                  be accessed using the 'get_SeqFeatures' method recursively.

        Example : # getting the complete hierarchy of features in a GFF3 file
                  my @toplevel_features;
                  while (my @fg = $stream->next_feature_group) {
                      push(@toplevel_features, @fg);
                  }
        Returns : an array of Bio::SeqFeature::Annotated objects
        Args    : none

   next_seq()
       access the FASTA section (if any) at the end of the GFF stream.  note that this method
       will return undef if not all features in the stream have been handled

   write_feature()
        Usage   : $featureio->write_feature( Bio::SeqFeature::Annotated->new(...) );
        Function: writes a feature in GFF format.  the GFF version used is governed by the
                  '-version' argument passed to Bio::FeatureIO->new(), and defaults to GFF
                  version 3.
        Returns : ###FIXME
        Args    : a Bio::SeqFeature::Annotated object.

ACCESSORS

   fasta_mode()
        Usage   : $obj->fasta_mode($newval)
        Function:
        Example :
        Returns : value of fasta_mode (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

       Side effect when setting: rewind the file handle a little bit to get the last carriage
       return that was swallowed when the previous line was processed.

   seqio()
        Usage   : $obj->seqio($newval)
        Function: holds a Bio::SeqIO instance for handling the GFF3 ##FASTA section.
        Returns : value of seqio (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   sequence_region()
        Usage   :
        Function: ###FIXME
        Returns :
        Args    :

   so()
        Usage   : $obj->so($newval)
        Function: holds a Sequence Ontology instance
        Returns : value of so (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   validate()
        Usage   : $obj->validate($newval)
        Function: true if encountered ontology terms in next_feature()
                  mode should be validated.
        Returns : value of validate (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   version()
        Usage   : $obj->version($newval)
        Function: version of GFF to read/write.  valid values are 1, 2, 2.5, and 3.
        Returns : value of version (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

INTERNAL METHODS

   _buffer_feature()
        Usage   :
        Function: ###FIXME
        Returns :
        Args    :

_handle_directive()

       this method is called for lines beginning with '##'.

_handle_feature()

       this method is called for each line not beginning with '#'.  it parses the line and
       returns a Bio::SeqFeature::Annotated object.

   _handle_non_reserved_tag()
        Usage   : $self->_handle_non_reserved_tag($feature,$tag,$value)
        Function: Deal with non-reserved word tags in the ninth column
        Returns : An updated Bio::SeqFeature::Annotated object
        Args    : A Bio::SeqFeature::Annotated and a tag/value pair

       Note that this method can be overridden in a subclass to provide special handling of non-
       reserved word tags.

   organism
       Gets/sets the organims from the organism directive

_write_feature_1()

       write a feature in GFF v1 format.  currently not implemented.

_write_feature_2()

       write a feature in GFF v2 format.  currently not implemented.

_write_feature_25()

       write a feature in GFF v2.5 (aka GTF) format.

_write_feature_3()

       write a feature in GFF v3 format.