Ewan Birney

NAME

Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser

SYNOPSIS

    use Bio::Tools::GFF;

    # specify input via -fh or -file
    my $gffio = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 2);
    my $feature;
    # loop over the input stream
    while($feature = $gffio->next_feature()) {
        # do something with feature
    }
    $gffio->close();

    # you can also obtain a GFF parser as a SeqAnalasisParserI in
    # HT analysis pipelines (see Bio::SeqAnalysisParserI and
    # Bio::Factory::SeqAnalysisParserFactory)
    my $factory = Bio::Factory::SeqAnalysisParserFactory->new();
    my $parser = $factory->get_parser(-input => \*STDIN, -method => "gff");
    while($feature = $parser->next_feature()) {
        # do something with feature
    }

DESCRIPTION

This class provides a simple GFF parser and writer. In the sense of a SeqAnalysisParser, it parses an input file or stream into SeqFeatureI objects, but is not in any way specific to a particular analysis program and the output that program produces.

That is, if you can get your analysis program spit out GFF, here is your result parser.

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 one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org          - General discussion
  http://bio.perl.org/MailList.html             - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHOR - Matthew Pocock

Email mrp@sanger.ac.uk

APPENDIX

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

new

 Title   : new
 Usage   : 
 Function: Creates a new instance. Recognized named parameters are -file, -fh,
           and -gff_version.

 Returns : a new object
 Args    : names parameters

next_feature

 Title   : next_feature
 Usage   : $seqfeature = $gffio->next_feature();
 Function: Returns the next feature available in the input file or stream, or
           undef if there are no more features.
 Example :
 Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
           more features.
 Args    : none    

from_gff_string

 Title   : from_gff_string
 Usage   : $gff->from_gff_string($feature, $gff_string);
 Function: Sets properties of a SeqFeatureI object from a GFF-formatted
           string. Interpretation of the string depends on the version
           that has been specified at initialization.

           This method is used by next_feature(). It actually dispatches to
           one of the version-specific (private) methods.
 Example :
 Returns : void
 Args    : A Bio::SeqFeatureI implementing object to be initialized
           The GFF-formatted string to initialize it from

_from_gff1_string

 Title   : _from_gff1_string
 Usage   :
 Function:
 Example :
 Returns : void
 Args    : A Bio::SeqFeatureI implementing object to be initialized
           The GFF-formatted string to initialize it from

_from_gff2_string

 Title   : _from_gff2_string
 Usage   :
 Function:
 Example :
 Returns : void
 Args    : A Bio::SeqFeatureI implementing object to be initialized
           The GFF2-formatted string to initialize it from

write_feature

 Title   : write_feature
 Usage   : $gffio->write_feature($feature);
 Function: Writes the specified SeqFeatureI object in GFF format to the stream
           associated with this instance.
 Example :
 Returns : 
 Args    : A Bio::SeqFeatureI implementing object to be serialized

gff_string

 Title   : gff_string
 Usage   : $gffstr = $gffio->gff_string($feature);
 Function: Obtain the GFF-formatted representation of a SeqFeatureI object.
           The formatting depends on the version specified at initialization.

           This method is used by write_feature(). It actually dispatches to
           one of the version-specific (private) methods.
 Example :
 Returns : A GFF-formatted string representation of the SeqFeature
 Args    : A Bio::SeqFeatureI implementing object to be GFF-stringified

_gff1_string

 Title   : _gff1_string
 Usage   : $gffstr = $gffio->_gff1_string
 Function: 
 Example :
 Returns : A GFF1-formatted string representation of the SeqFeature
 Args    : A Bio::SeqFeatureI implementing object to be GFF-stringified

_gff2_string

 Title   : _gff2_string
 Usage   : $gffstr = $gffio->_gff2_string
 Function: 
 Example :
 Returns : A GFF2-formatted string representation of the SeqFeature
 Args    : A Bio::SeqFeatureI implementing object to be GFF2-stringified

gff_version

 Title   : _gff_version
 Usage   : $gffversion = $gffio->gff_version
 Function: 
 Example :
 Returns : The GFF version this parser will accept and emit.
 Args    : none