Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser use Bio::Tool::GFF; # specify input via -fh or -file my $gffio = Bio::Tools::GFF(-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 } 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.

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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/ Email mrp@sanger.ac.uk 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