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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 GFFParser - simple gff3 parser.
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16
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17
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18 =head1 AUTHOR
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19
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20 Monika Komorowska, 2012 - monika@ebi.ac.uk
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21
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22 =head1 SYNOPSIS
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23
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24 use strict;
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25 use Bio::EnsEMBL::Utils::IO::GFFParser;
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26 use IO::File;
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27
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28 my $file_name = "features.gff";
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29 my $fh = IO::File->new($file_name, 'r');
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30 my $parser = Bio::EnsEMBL::Utils::IO::GFFParser->new($fh);
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31
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32 my @header_lines = @{$parser->parse_header()};
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33 #do something with the header lines array, e.g. print array elements
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34
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35 foreach my $header_line (@header_lines) {
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36 print $header_line . "\n";
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37 }
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38 print "\n\n";
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39 my $feature = $parser->parse_next_feature();
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40
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41 while (defined($feature) ) {
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42
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43 my %feature = %{$feature};
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44
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45 #do something with the feature, e.g. print hash keys and values
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46 foreach my $key (keys %feature) {
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47 if ($key ne 'attribute') {
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48 print $key . " " . $feature{$key} ."\n";
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49 } else {
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50 print $key . "\n";
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51 my %attribs = %{$feature{$key}};
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52 foreach my $attrib_key (keys %attribs) {
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53 printf("\t%s %s\n", $attrib_key, join(q{, }, @{wrap_array($values)}));
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54
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55 }
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56 }
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57 }
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58 print "\n\n";
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59 $feature = $parser->parse_next_feature();
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60 }
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61
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62 my $sequence = $parser->parse_next_sequence();
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63
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64 while (defined($sequence)) {
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65 my %sequence = %{$sequence};
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66
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67 foreach my $key (keys %sequence) {
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68 print $key . " " . $sequence{$key} ."\n";
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69 }
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70 print "\n\n";
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71
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72 $sequence = $parser->parse_next_sequence();
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73 }
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74
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75 $parser->close();
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76
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77 $fh->close();
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78
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79
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80
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81 =head1 DESCRIPTION
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82
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83 GFF3 format as defined in http://www.sequenceontology.org/gff3.shtml
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84
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85 Use parse_header method to parse a GFF3 file header, and parse_next_feature to parse the next feature line in the file.
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86
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87 This class can be extended to convert a feature hash into a feature object reversing
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88 the processing done by GFFSerializer.
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89
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90 =cut
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91
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92 package Bio::EnsEMBL::Utils::IO::GFFParser;
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93 use strict;
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94 use warnings;
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95 use Bio::EnsEMBL::Utils::Exception;
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96 use IO::File;
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97 use URI::Escape;
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98 use Bio::EnsEMBL::Utils::Scalar qw/wrap_array/;
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99
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100
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101 my %strand_conversion = ( '+' => '1', '?' => '0', '-' => '-1');
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102
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103 =head2 new
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104
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105 Constructor
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106 Arg [1] : File handle
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107
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108 Returntype : Bio::EnsEMBL::Utils::IO::GFFParser
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109
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110 =cut
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111
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112 sub new {
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113 my $class = shift;
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114 my $self = {
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115 filehandle => shift,
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116 };
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117 bless $self, $class;
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118 if (!defined($self->{'filehandle'})) {
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119 throw("GFFParser requires a valid filehandle to a GFF3 formatted file");
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120 }
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121 return $self;
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122
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123 }
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124
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125 =head2 parse_header
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126
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127 Arg [1] : File handle
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128 Description: Returns a arrayref with each header line stored in array element
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129 Returntype : Arrayref of GFF3 file header lines
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130
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131 =cut
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132
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133 sub parse_header {
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134
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135 my $self = shift;
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136
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137 my $next_line;
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138 my @header_lines;
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139
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140 while (($next_line = $self->_read_line()) && ($next_line =~ /^[\#|\s]/) ) {
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141
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142 #stop parsing features if ##FASTA directive encountered
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143 last if ($next_line =~ /\#\#FASTA/ );
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144
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145 #header lines start with ## (except for the ##FASTA directive indicating sequence section)
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146 if ($next_line =~ /^[\#]{2}/ ) {
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147 push @header_lines, $next_line;
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148 if ($next_line =~ /gff-version\s+(\d+)/) {
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149 if ($1 != 3) {
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150 warning("File has been formatted in GFF version $1. GFFParser may return unexpected results as it is designed to parse GFF3 formatted files.");
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151 }
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152 }
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153 }
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154 }
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155
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156 if (defined($next_line)) {
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157 $self->{'first_non_header_line'} = $next_line;
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158 }
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159 return \@header_lines;
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160
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161 }
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162
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163 =head2 parse_next_feature
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164
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165 Arg [1] : File handle
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166 Description: Returns a hashref in the format -
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167 {
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168 seqid => scalar,
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169 source => scalar,
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170 type => scalar,
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171 start => scalar,
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172 end => scalar,
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173 score => scalar,
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174 strand => scalar,
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175 phase => scalar,
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176 attribute => hashref,
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177
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178 }
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179 Returntype : Hashref of a GFF3 feature line
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180
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181 =cut
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182
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183 sub parse_next_feature {
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184
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185 my $self = shift;
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186
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187 my $next_line;
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188 my $feature_line;
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189
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190 while (($next_line = $self->_read_line() ) && defined($next_line) ) {
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191
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192 #stop parsing features if ##FASTA directive
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193 last if ($next_line =~ /\#\#FASTA/);
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194
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195
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196 next if ($next_line =~ /^\#/ || $next_line =~ /^\s*$/ ||
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197 $next_line =~ /^\/\//);
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198
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199 $feature_line = $next_line;
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200 last;
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201 }
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202
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203 return undef unless $feature_line;
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204
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205 my %feature;
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206 my %attribute;
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207
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208
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209 #strip off trailing comments
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210 $feature_line =~ s/\#.*//;
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211
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212 my @chunks = split(/\t/, $feature_line);
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213
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214 %feature = (
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215 'seqid' => uri_unescape($chunks[0]),
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216 'source' => uri_unescape($chunks[1]),
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217 'type' => uri_unescape($chunks[2]),
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218 'start' => $chunks[3],
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219 'end' => $chunks[4],
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220 'score' => $chunks[5],
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221 'strand' => $strand_conversion{$chunks[6]},
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222 'phase' => $chunks[7]
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223 );
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224
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225 if ($chunks[8]) {
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226 my @attributes = split( /;/, $chunks[8] );
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227 my %attributes;
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228 foreach my $attribute (@attributes) {
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229 my ( $name, $value ) = split( /=/, $attribute );
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230 $name = uri_unescape($name);
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231 my @split_values = map { uri_unescape($_) } split(/,/, $value);
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232 if(scalar(@split_values) > 1) {
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233 $attributes{$name} = \@split_values;
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234 }
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235 else {
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236 $attributes{$name} = $split_values[0];
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237 }
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238 }
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239 $feature{'attribute'} = \%attributes;
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240 }
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241
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242 return \%feature;
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243 }
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244
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245 =head2 parse_next_sequence
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246
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247 Arg [1] : File handle
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248 Description: Returns a hashref in the format -
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249 {
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250 header => scalar,
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251 sequence => scalar,
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252
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253 }
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254 Returntype : Hashref of a GFF3 sequence line
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255
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256 =cut
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257
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258 sub parse_next_sequence {
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259
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260 my $self = shift;
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261
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262 my $next_line;
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263 my $sequence;
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264 my $header;
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265
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266 while (($next_line = $self->_read_line() ) && defined($next_line) ) {
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267
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268 next if ($next_line =~ /^\#/ || $next_line =~ /^\s*$/ ||
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269 $next_line =~ /^\/\//);
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270
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271 if ($next_line =~ /^>/) {
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272 if ($header) {
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273 #next fasta header encountered
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274 $self->{'next_fasta_header'} = $next_line;
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275 last;
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276
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277 } else {
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278 $header = $next_line;
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279 }
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280 } else {
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281 $sequence .= $next_line;
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282 }
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283 }
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284
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285 return undef unless ($sequence || $header);
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286
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287 my %sequence = (header => $header , sequence => $sequence );
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288
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289 return \%sequence;
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290 }
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291
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292
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293 sub _read_line {
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294
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295 my $self = shift;
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296 my $fh = $self->{'filehandle'};
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297
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298 my $line;
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299
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300 if (defined($self->{'first_non_header_line'})) {
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301 $line = $self->{'first_non_header_line'};
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302 $self->{'first_non_header_line'} = undef;
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303 } elsif ( defined($self->{'next_fasta_header'} )) {
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304 $line = $self->{'next_fasta_header'};
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305 $self->{'next_fasta_header'} = undef;
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306 }
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307 else {
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308 $line = <$fh>;
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309 if (defined($line)) {
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310 chomp $line;
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311 if (!$line) {
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312 #parse next line if current line is empty
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313 $line = $self->_read_line();
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314 }
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315 }
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316 }
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317
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318 return $line;
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319 }
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320
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321 sub close {
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322
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323 my $self = shift;
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324 $self->{"filehandle"} = undef;
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325
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326 }
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327
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328 1;
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