diff variant_effect_predictor/Bio/EnsEMBL/Utils/IO/GFFSerializer.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Utils/IO/GFFSerializer.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,217 @@
+=pod
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 NAME
+
+GFFSerializer - Feature to GFF converter
+
+=head1 AUTHOR
+
+Kieron Taylor, 2011 - [e-mail]
+
+=head1 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);
+
+=head1 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.
+
+=cut
+
+package Bio::EnsEMBL::Utils::IO::GFFSerializer;
+use strict;
+use warnings;
+use Bio::EnsEMBL::Utils::Exception;
+use Bio::EnsEMBL::Utils::BiotypeMapper;
+use URI::Escape;
+use Bio::EnsEMBL::Utils::IO::FeatureSerializer;
+
+use base qw(Bio::EnsEMBL::Utils::IO::FeatureSerializer);
+
+my %strand_conversion = ( '1' => '+', '0' => '?', '-1' => '-');
+
+=head2 new
+
+    Constructor
+    Arg [1]    : Ontology Adaptor
+    Arg [2]    : Optional File handle
+    
+    Returntype : Bio::EnsEMBL::Utils::IO::GFFSerializer
+
+=cut
+
+sub new {
+    my $class = shift;
+    my $self = {
+        ontology_adaptor => shift,
+        filehandle => shift,
+    };
+    bless $self, $class;
+    if ( ref($self->{'ontology_adaptor'}) ne "Bio::EnsEMBL::DBSQL::OntologyTermAdaptor" ) {
+        throw("GFF format requires an instance of Bio::EnsEMBL::DBSQL::OntologyTermAdaptor to function. See also Bio::EnsEMBL::Utils::BiotypeMapper");        
+    }
+    $self->{'mapper'} = new Bio::EnsEMBL::Utils::BiotypeMapper($self->{'ontology_adaptor'});
+    
+    if (!defined ($self->{'filehandle'})) {
+        # no file handle, let the handle point to a copy of STDOUT instead
+        open $self->{'filehandle'}, ">&STDOUT";
+        $self->{'stdout'} = 1;
+    }
+    return $self;
+}
+
+=head2 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
+=cut
+
+sub print_feature {
+    my $self = shift;
+    my $feature = shift;
+    my $biotype_mapper = $self->{'mapper'};
+
+    my $text_buffer = "";
+    if ($feature->can('summary_as_hash') ) {
+        my %summary = %{$feature->summary_as_hash};
+        my $row = "";
+#    Column 1 - seqname, the name of the sequence/chromosome the feature is on. Landmark for start below
+        if (!defined($summary{'seq_region_name'})) {$summary{'seq_region_name'} = "?";}
+        $row .= $summary{'seq_region_name'}."\t";
+
+#    Column 2 - source, complicated with Ensembl not being the originator of all data
+        $row .= "EnsEMBL\t";
+
+#   Column 3 - feature, the ontology term for the kind of feature this row is
+        my $so_term = $biotype_mapper->translate_feature_to_SO_term($feature);
+        $row .= $so_term."\t";
+
+#    Column 4 - start, the start coordinate of the feature, here shifted to chromosomal coordinates
+#    Start and end must be in ascending order for GFF. Circular genomes require the length of 
+#   the circuit to be added on.
+        if ($summary{'start'} > $summary{'end'}) {
+            #assumes this is not a Compara circular sequence and can treat is as a Feature
+            if ($feature->slice() && $feature->slice()->is_circular() ) {
+                $summary{'end'} = $summary{'end'} + $feature->seq_region_length;
+            }
+            # non-circular, but end still before start
+            else {$summary{'end'} = $summary{'start'};}
+        }
+        $row .= $summary{'start'} . "\t";
+
+#    Column 5 - end, coordinates (absolute) for the end of this feature
+        $row .= $summary{'end'} . "\t";
+
+#    Column 6 - score, for variations only.
+        if (exists($summary{'score'})) {
+            $row .= $summary{'score'}."\t";
+        }
+        else {
+            $row .= ".\t";
+        }
+
+#    Column 7 - strand, up or down
+        if (exists($summary{'strand'})) {
+            $row .= $strand_conversion{$summary{'strand'}}."\t";
+        }
+        else {
+            $row .= ".\t";
+        }
+
+#   Column 8 - reading frame, necessary only for Exons
+        $row .= ".\t";
+
+#    Column 9 - the 'other' section for all GFF and GVF compliant attributes
+#    We include Stable ID and biotype where possible to supplement the information in the other columns
+        delete $summary{'seq_region_start'};
+        delete $summary{'seq_region_name'};
+        delete $summary{'start'};
+        delete $summary{'end'};
+        delete $summary{'strand'};
+        delete $summary{'score'};
+#   Slice the hash for specific keys in GFF-friendly order
+        my @ordered_keys = qw(ID Name Alias Parent Target Gap Derives_from Note Dbxref Ontology_term Is_circular);
+        my @ordered_values = @summary{@ordered_keys};
+        while (my $key = shift @ordered_keys) {
+            my $value = shift @ordered_values;
+            if ($value) {
+                $row .= $key."=".uri_escape($value,'\t\n\r;=%&,').";";
+            }
+            delete $summary{$key};
+        }
+#   Catch the remaining keys, containing whatever else the Feature provided
+        foreach my $attribute ( keys(%summary)) {
+            if (ref $summary{$attribute} eq "ARRAY") {
+                $row .= $attribute."=".join (',',@{$summary{$attribute}}) . ";"
+            }
+            else {
+                if ($summary{$attribute}) { $row .= $attribute."=".uri_escape($summary{$attribute},'\t\n\r;=%&,') . ";"; }
+            }
+        }
+# trim off any trailing commas left by the ordered keys stage above:
+        $text_buffer .= $row."\n";
+    }
+    else {
+        warning("Feature failed to self-summarise");
+    }
+    #filehandle is inherited
+    my $fh = $self->{'filehandle'};
+    print $fh $text_buffer;
+}
+
+=head2 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
+=cut
+
+sub print_main_header {
+    my $self = shift;
+    my $arrayref_of_slices = shift;
+    my $fh = $self->{'filehandle'};
+    
+    print $fh "##gff-version 3\n";
+    foreach my $slice (@{$arrayref_of_slices}) {
+        if (not defined($slice)) { warning("Slice not defined.\n"); return;}
+        print $fh "##sequence-region   ",$slice->seq_region_name," ",$slice->start," ",$slice->end,"\n";
+    }
+}
+
+sub print_metadata {
+    my $self = shift;
+    my $text = shift;
+    my $fh = $self->{'filehandle'};
+    print $fh "\n#".$text."\n";
+}
+
+
+1;