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1 =pod
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2
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3 =head1 LICENSE
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4
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5 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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6 Genome Research Limited. All rights reserved.
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7
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8 This software is distributed under a modified Apache license.
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9 For license details, please see
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10
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11 http://www.ensembl.org/info/about/code_licence.html
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12
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13 =head1 NAME
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14
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15 GFFSerializer - Feature to GFF converter
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16
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17 =head1 AUTHOR
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18
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19 Kieron Taylor, 2011 - ktaylor@ebi.ac.uk
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20
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21 =head1 SYNOPSIS
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22
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23 use Bio::EnsEMBL::Utils::IO::GFFSerializer;
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24 use Bio::EnsEMBL::Utils::BiotypeMapper;
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25
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26 my $ontology_adaptor = $registry->get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );
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27 my $biotype_mapper = new BiotypeMapper($ontology_adaptor);
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28 my $serializer = new GFFSerializer($biotype_mapper,$output_fh);
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29
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30 my $variation_feature_adaptor = $registry->get_adaptor( $config{'species'}, 'variation', 'variationfeature' );
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31 $serializer->print_metadata("Variation Features:");
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32 my $iterator = $variation_feature_adaptor->fetch_Iterator_by_Slice($slice,undef,60000);
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33 $serializer->print_feature_Iterator($iterator);
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34
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35 =head1 DESCRIPTION
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36
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37 Subclass of Serializer that can turn a feature into a line for the GFF3 format. Requires
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38 a BiotypeMapper in order to translate biotypes to SO terms.
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39
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40 =cut
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41
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42 package Bio::EnsEMBL::Utils::IO::GFFSerializer;
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43 use strict;
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44 use warnings;
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45 use Bio::EnsEMBL::Utils::Exception;
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46 use Bio::EnsEMBL::Utils::BiotypeMapper;
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47 use URI::Escape;
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48 use Bio::EnsEMBL::Utils::IO::FeatureSerializer;
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49
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50 use base qw(Bio::EnsEMBL::Utils::IO::FeatureSerializer);
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51
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52 my %strand_conversion = ( '1' => '+', '0' => '?', '-1' => '-');
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53
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54 =head2 new
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55
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56 Constructor
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57 Arg [1] : Ontology Adaptor
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58 Arg [2] : Optional File handle
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59
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60 Returntype : Bio::EnsEMBL::Utils::IO::GFFSerializer
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61
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62 =cut
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63
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64 sub new {
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65 my $class = shift;
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66 my $self = {
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67 ontology_adaptor => shift,
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68 filehandle => shift,
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69 };
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70 bless $self, $class;
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71 if ( ref($self->{'ontology_adaptor'}) ne "Bio::EnsEMBL::DBSQL::OntologyTermAdaptor" ) {
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72 throw("GFF format requires an instance of Bio::EnsEMBL::DBSQL::OntologyTermAdaptor to function. See also Bio::EnsEMBL::Utils::BiotypeMapper");
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73 }
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74 $self->{'mapper'} = new Bio::EnsEMBL::Utils::BiotypeMapper($self->{'ontology_adaptor'});
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75
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76 if (!defined ($self->{'filehandle'})) {
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77 # no file handle, let the handle point to a copy of STDOUT instead
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78 open $self->{'filehandle'}, ">&STDOUT";
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79 $self->{'stdout'} = 1;
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80 }
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81 return $self;
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82 }
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83
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84 =head2 print_feature
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85
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86 Arg [1] : Bio::EnsEMBL::Feature, subclass or related pseudo-feature
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87 Example : $reporter->print_feature($feature,$slice_start_coordinate,"X")
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88 Description: Asks a feature for its summary, and generates a GFF3
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89 compliant entry to hand back again
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90 Additional attributes are handed through to column 9 of the
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91 output using exact spelling and capitalisation of the
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92 feature-supplied hash.
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93 Returntype : none
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94 =cut
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95
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96 sub print_feature {
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97 my $self = shift;
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98 my $feature = shift;
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99 my $biotype_mapper = $self->{'mapper'};
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100
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101 my $text_buffer = "";
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102 if ($feature->can('summary_as_hash') ) {
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103 my %summary = %{$feature->summary_as_hash};
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104 my $row = "";
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105 # Column 1 - seqname, the name of the sequence/chromosome the feature is on. Landmark for start below
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106 if (!defined($summary{'seq_region_name'})) {$summary{'seq_region_name'} = "?";}
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107 $row .= $summary{'seq_region_name'}."\t";
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108
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109 # Column 2 - source, complicated with Ensembl not being the originator of all data
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110 $row .= "EnsEMBL\t";
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111
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112 # Column 3 - feature, the ontology term for the kind of feature this row is
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113 my $so_term = $biotype_mapper->translate_feature_to_SO_term($feature);
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114 $row .= $so_term."\t";
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115
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116 # Column 4 - start, the start coordinate of the feature, here shifted to chromosomal coordinates
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117 # Start and end must be in ascending order for GFF. Circular genomes require the length of
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118 # the circuit to be added on.
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119 if ($summary{'start'} > $summary{'end'}) {
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120 #assumes this is not a Compara circular sequence and can treat is as a Feature
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121 if ($feature->slice() && $feature->slice()->is_circular() ) {
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122 $summary{'end'} = $summary{'end'} + $feature->seq_region_length;
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123 }
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124 # non-circular, but end still before start
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125 else {$summary{'end'} = $summary{'start'};}
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126 }
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127 $row .= $summary{'start'} . "\t";
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128
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129 # Column 5 - end, coordinates (absolute) for the end of this feature
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130 $row .= $summary{'end'} . "\t";
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131
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132 # Column 6 - score, for variations only.
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133 if (exists($summary{'score'})) {
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134 $row .= $summary{'score'}."\t";
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135 }
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136 else {
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137 $row .= ".\t";
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138 }
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139
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140 # Column 7 - strand, up or down
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141 if (exists($summary{'strand'})) {
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142 $row .= $strand_conversion{$summary{'strand'}}."\t";
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143 }
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144 else {
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145 $row .= ".\t";
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146 }
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147
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148 # Column 8 - reading frame, necessary only for Exons
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149 $row .= ".\t";
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150
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151 # Column 9 - the 'other' section for all GFF and GVF compliant attributes
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152 # We include Stable ID and biotype where possible to supplement the information in the other columns
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153 delete $summary{'seq_region_start'};
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154 delete $summary{'seq_region_name'};
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155 delete $summary{'start'};
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156 delete $summary{'end'};
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157 delete $summary{'strand'};
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158 delete $summary{'score'};
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159 # Slice the hash for specific keys in GFF-friendly order
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160 my @ordered_keys = qw(ID Name Alias Parent Target Gap Derives_from Note Dbxref Ontology_term Is_circular);
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161 my @ordered_values = @summary{@ordered_keys};
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162 while (my $key = shift @ordered_keys) {
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163 my $value = shift @ordered_values;
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164 if ($value) {
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165 $row .= $key."=".uri_escape($value,'\t\n\r;=%&,').";";
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166 }
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167 delete $summary{$key};
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168 }
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169 # Catch the remaining keys, containing whatever else the Feature provided
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170 foreach my $attribute ( keys(%summary)) {
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171 if (ref $summary{$attribute} eq "ARRAY") {
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172 $row .= $attribute."=".join (',',@{$summary{$attribute}}) . ";"
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173 }
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174 else {
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175 if ($summary{$attribute}) { $row .= $attribute."=".uri_escape($summary{$attribute},'\t\n\r;=%&,') . ";"; }
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176 }
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177 }
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178 # trim off any trailing commas left by the ordered keys stage above:
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179 $text_buffer .= $row."\n";
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180 }
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181 else {
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182 warning("Feature failed to self-summarise");
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183 }
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184 #filehandle is inherited
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185 my $fh = $self->{'filehandle'};
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186 print $fh $text_buffer;
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187 }
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188
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189 =head2 print_main_header
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190
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191 Arg [1] : Arrayref of slices going into the file.
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192 Description: Printing the header text or metadata required for GFF,
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193 using a list of slices to be written
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194 Returntype : None
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195 =cut
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196
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197 sub print_main_header {
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198 my $self = shift;
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199 my $arrayref_of_slices = shift;
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200 my $fh = $self->{'filehandle'};
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201
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202 print $fh "##gff-version 3\n";
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203 foreach my $slice (@{$arrayref_of_slices}) {
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204 if (not defined($slice)) { warning("Slice not defined.\n"); return;}
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205 print $fh "##sequence-region ",$slice->seq_region_name," ",$slice->start," ",$slice->end,"\n";
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206 }
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207 }
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208
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209 sub print_metadata {
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210 my $self = shift;
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211 my $text = shift;
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212 my $fh = $self->{'filehandle'};
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213 print $fh "\n#".$text."\n";
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214 }
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215
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216
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217 1;
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