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Bio::EnsEMBL::Utils::IO::GFFSerializer Class Reference
Inheritance diagram for Bio::EnsEMBL::Utils::IO::GFFSerializer:

List of all members.


Class Summary

Synopsis

use Bio::EnsEMBL::Utils::IO::GFFSerializer;
use Bio::EnsEMBL::Utils::BiotypeMapper;

my $ontology_adaptor = $registry-\>get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );
my $biotype_mapper = new BiotypeMapper($ontology_adaptor);
my $serializer = new GFFSerializer($biotype_mapper,$output_fh);

my $variation_feature_adaptor = $registry-\>get_adaptor( $config{'species'}, 'variation', 'variationfeature' );
$serializer-\>print_metadata("Variation Features:");
my $iterator = $variation_feature_adaptor-\>fetch_Iterator_by_Slice($slice,undef,60000);
$serializer-\>print_feature_Iterator($iterator);

Description

Subclass of Serializer that can turn a feature into a line for the GFF3 format. Requires
a BiotypeMapper in order to translate biotypes to SO terms.
 

Definition at line 31 of file GFFSerializer.pm.

Available Methods

public DESTROY ()
public void formatted_write ()
public
Bio::EnsEMBL::Utils::IO::GFFSerializer 
new ()
public void print_feature ()
public void print_feature_Iterator ()
public print_feature_list ()
public void print_main_header ()
public print_metadata ()
public print_sequence ()
public Boolean printed_something ()

Method Documentation

public Bio::EnsEMBL::Utils::IO::Serializer::DESTROY ( ) [inherited]
	Destructor
	Description: Restores default state of the STDOUT filehandle as it is a copy
	             and may not flush correctly.
 
Code:
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public void Bio::EnsEMBL::Utils::IO::Serializer::formatted_write ( ) [inherited]
   Arg [1]    : Line format, see Perldoc of formline()
   Arg [2]    : Array of arguments to suit the line format in Arg [1]
   Description: Writes data to the filehandle and rigidly formats it.
                Refer to Perldoc on formline() to specify valid formats.
                Useful for fixed-width file formats.
                Suicides in the event of file system issues.
   Example    : my $FORMAT = '^<<<<<<<<<<<<<<<<<<<|<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n';
                $serializer->formatted_write($FORMAT,@text_fields);
   Returntype : None
 
Code:
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public Bio::EnsEMBL::Utils::IO::GFFSerializer Bio::EnsEMBL::Utils::IO::GFFSerializer::new ( )
    Constructor
    Arg [1]    : Ontology Adaptor
    Arg [2]    : Optional File handle
    Returntype : Bio::EnsEMBL::Utils::IO::GFFSerializer
 
Code:
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Reimplemented from Bio::EnsEMBL::Utils::IO::Serializer.

public void Bio::EnsEMBL::Utils::IO::GFFSerializer::print_feature ( )
    Arg [1]    : Bio::EnsEMBL::Feature, subclass or related pseudo-feature
    Example    : $reporter->print_feature($feature,$slice_start_coordinate,"X")
    Description: Asks a feature for its summary, and generates a GFF3 
                 compliant entry to hand back again
                 Additional attributes are handed through to column 9 of the 
                 output using exact spelling and capitalisation of the 
                 feature-supplied hash.
    Returntype : none
 
Code:
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Reimplemented from Bio::EnsEMBL::Utils::IO::FeatureSerializer.

public void Bio::EnsEMBL::Utils::IO::FeatureSerializer::print_feature_Iterator ( ) [inherited]
	Arg [1]    : Bio::EnsEMBL::Utils::Iterator
	Description: Automatically spools through an iterator for convenience
	Returntype : None
 
Code:
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public Bio::EnsEMBL::Utils::IO::FeatureSerializer::print_feature_list ( ) [inherited]
	Arg [1]    : Listref of Features
	Description: Run print_feature on every feature in the list
 
Code:
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Reimplemented in Bio::EnsEMBL::Utils::IO::ReportSerializer.

public void Bio::EnsEMBL::Utils::IO::GFFSerializer::print_main_header ( )
    Arg [1]    : Arrayref of slices going into the file.
    Description: Printing the header text or metadata required for GFF,
                 using a list of slices to be written
    Returntype : None
 
Code:
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Reimplemented from Bio::EnsEMBL::Utils::IO::Serializer.

public Bio::EnsEMBL::Utils::IO::GFFSerializer::print_metadata ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Utils::IO::Serializer.

public Bio::EnsEMBL::Utils::IO::Serializer::print_sequence ( ) [inherited]
	Arg [1]    : Bio::EnsEMBL::Slice
	Description: By default, prints a block of FASTA format sequence from the given slice

Deprecated:
Code:
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public Boolean Bio::EnsEMBL::Utils::IO::Serializer::printed_something ( ) [inherited]
    Description: Check if serializer has printed any useful data. Not accurate with FASTA
                 due to non-reporting dumper.
    Returntype : Boolean
 
Code:
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The documentation for this class was generated from the following file: