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.
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
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
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : Function: Creates a new instance. Recognized named parameters are -file, -fh, and -gff_version. Returns : a new object Args : names parameters
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
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
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
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
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
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
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
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
Title : _gff_version Usage : $gffversion = $gffio->gff_version Function: Example : Returns : The GFF version this parser will accept and emit. Args : none
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 :
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
To install LocalConfig, copy and paste the appropriate command in to your terminal.
cpanm
cpanm LocalConfig
CPAN shell
perl -MCPAN -e shell install LocalConfig
For more information on module installation, please visit the detailed CPAN module installation guide.