Bio::Tools::GFF - A Bio::SeqAnalysisParserI compliant GFF format parser 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 } 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. While Bio::Tools::GFF supports GFF3, it does not deal with sequence data, which is valid in GFF3. If you want to use Bio::Tools::GFF with GFF3 that has sequence data, the sequence must be removed before analysis.

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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://bugzilla.bioperl.org/ Email mrp@sanger.ac.uk Jason Stajich, jason-at-biperl-dot-org 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

_parse_header
Title : _parse_header Usage : $gffio->_parse_header() Function: used to turn parse GFF header lines. currently produces Bio::LocatableSeq objects from ##sequence-region lines Example : Returns : 1 on success Args : none

next_segment
Title : next_segment Usage : my $seq = $gffio->next_segment; Function: Returns a Bio::LocatableSeq object corresponding to a GFF "##sequence-region" header line. Example : Returns : A Bio::LocatableSeq object, or undef if there are no more sequences. Args : none

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. Returns : none Args : An array of Bio::SeqFeatureI implementing objects 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

_gff3_string
Title : _gff3_string Usage : $gffstr = $gffio->_gff3_string Function: Example : Returns : A GFF3-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

newFh
Title : newFh Usage : $fh = Bio::Tools::GFF->newFh(-file=>$filename,-format=>'Format') Function: does a new() followed by an fh() Example : $fh = Bio::Tools::GFF->newFh(-file=>$filename,-format=>'Format') $feature = <$fh>; # read a feature object print $fh $feature ; # write a feature object Returns : filehandle tied to the Bio::Tools::GFF class Args :

fh
Title : fh Usage : $obj->fh Function: Example : $fh = $obj->fh; # make a tied filehandle $feature = <$fh>; # read a feature object print $fh $feature; # write a feature object Returns : filehandle tied to Bio::Tools::GFF class Args : none