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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 =head1 NAME
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22
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23 Bio::EnsEMBL::TranscriptFactory - Module having the fset2transcript*
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24 subroutines
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25
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26 =head1 SYNOPSIS
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27
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28 use Bio::EnsEMBL::TranscriptFactory;
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29
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30 &Bio::EnsEMBL::TranscriptFactory::fset2transcript($fset_id);
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31
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32 =head1 DESCRIPTION
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33
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34 Module containing the subroutines fset2transcript*,
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35 which create transcripts from features (formally housed in
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36 Bio::EnsEMBL::DBSQL::Utils).
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37
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38 =head1 METHODS
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39
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40 =cut
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41
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42 package Bio::EnsEMBL::TranscriptFactory;
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43
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44 use strict;
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45
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46 use Bio::EnsEMBL::Exon;
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47 use Bio::EnsEMBL::Translation;
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48 use Bio::EnsEMBL::Transcript;
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49
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50 sub fset2transcript {
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51 my ($genscan,$contig)=@_;
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52
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53
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54 unless ($genscan->isa ("Bio::EnsEMBL::SeqFeatureI"))
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55 {print "$genscan must be Bio::EnsEMBL::SeqFeatureI\n";}
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56
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57 my $transcript = new Bio::EnsEMBL::Transcript;
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58 $transcript->temporary_id($contig->id . "." . $genscan->seqname);
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59
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60 my @exons;
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61 my $count= 1;
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62
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63 foreach my $f ($genscan->sub_SeqFeature) {
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64
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65 my $exon = new Bio::EnsEMBL::Exon;
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66 $transcript->add_Exon($exon);
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67 $exon->contig ($contig);
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68 $exon->start ($f->start);
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69 $exon->end ($f->end );
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70 $exon->strand ($f->strand);
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71 $exon->phase ($f->phase);
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72 $exon->end_phase( ($exon->phase + $exon->length)%3 );
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73 #$exon->score($f->score);
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74 # $exon->p_value($f->p_value);
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75 $exon->slice($contig->primary_seq);
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76
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77 push(@exons,$exon);
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78 $count++;
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79
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80 }
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81
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82 if( $count == 1 ) {
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83 $genscan->throw("Got a 0 exon genscan");
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84 }
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85
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86 my $translation = new Bio::EnsEMBL::Translation;
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87 #
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88 # This code got changed due to Translation convention changing. Should work...
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89 #
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90
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91 if ($exons[0]->strand == 1) {
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92 @exons = sort {$a->start <=> $b->start} @exons;
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93 } else {
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94 @exons = sort {$b->start <=> $a->start} @exons;
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95 }
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96
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97 $translation->start(1);
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98 $translation->end($exons[scalar(@exons)-1]->length);
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99
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100 $translation->start_Exon($exons[0]);
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101 $translation->end_Exon($exons[$#exons]);
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102
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103 my $endphase = $exons[0]->end_phase;
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104
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105 foreach my $exon (@exons) {
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106
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107 if ( $exon == $exons[0] ){
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108 next;
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109 }
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110 $exon->phase ($endphase);
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111 $endphase = $exon->end_phase;
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112 }
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113
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114 $transcript->translation($translation);
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115
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116 return $transcript;
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117 }
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118
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119 sub fset2transcript_guess_phases {
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120 my ($fset,$contig) = @_;
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121
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122 my $transcript = new Bio::EnsEMBL::Transcript;
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123
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124 $transcript->temporary_id($contig->id . "." . $fset->id);
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125
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126
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127 my @exons;
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128 my $count = 1;
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129
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130 foreach my $f ($fset->sub_SeqFeature) {
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131
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132 my $exon = new Bio::EnsEMBL::Exon;
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133 $exon->contig ($contig);
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134 $exon->start ($f->start);
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135 $exon->end ($f->end );
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136 $exon->strand ($f->strand);
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137 #$exon->score($f->score);
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138 # $exon->p_value($f->p_value);
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139 $exon->slice($contig);
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140 $exon->phase($f->phase);
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141 push(@exons,$exon);
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142 $count++;
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143
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144 }
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145
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146 my $translation = new Bio::EnsEMBL::Translation;
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147
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148 if ($exons[0]->strand == 1) {
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149 @exons = sort {$a->start <=> $b->start} @exons;
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150 } else {
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151 @exons = sort {$b->start <=> $a->start} @exons;
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152 }
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153
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154 $translation->start (1);
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155 $translation->end ($exons[$#exons]->end - $exons[$#exons]->start + 1);
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156 $translation->start_Exon($exons[0]);
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157 $translation->end_Exon($exons[$#exons]);
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158 $transcript->translation($translation);
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159
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160 my $endphase = 0;
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161
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162 foreach my $exon (@exons) {
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163
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164 $exon ->phase ($endphase);
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165 $transcript->add_Exon($exon);
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166
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167 $endphase = $exon->end_phase(($exon->phase + $exon->length)%3);
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168
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169 }
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170
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171
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172 if ($transcript->translate->seq !~ /\*/) {
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173 return $transcript;
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174 }
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175
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176 $endphase = 1;
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177
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178 foreach my $exon (@exons) {
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179 $exon->phase($endphase);
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180 $endphase = $exon->end_phase(($exon->phase + $exon->length)%3);
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181 }
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182
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183 if ($transcript->translate->seq !~ /\*/) {
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184 return $transcript;
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185 }
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186
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187 $endphase = 2;
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188
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189 foreach my $exon (@exons) {
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190 $exon->phase($endphase);
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191 $endphase = $exon->end_phase(($exon->phase + $exon->length)%3);
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192 }
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193
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194 if ($transcript->translate->seq !~ /\*/) {
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195 return $transcript;
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196 }
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197 }
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198
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199 sub fset2transcript_3frame {
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200 my ($fset,$contig) = @_;
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201
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202 my @f = $fset->sub_SeqFeature;
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203
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204 if ($f[0]->strand == 1) {
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205 @f = sort {$a->start <=> $b->start} @f;
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206 } else {
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207 @f = sort {$b->start <=> $a->start} @f;
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208 }
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209
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210 my @transcripts;
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211
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212 my $startphase = 0;
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213
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214 while ($startphase < 3) {
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215 my $endphase = $startphase;
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216
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217 my $transcript = new Bio::EnsEMBL::Transcript;
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218
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219 push(@transcripts,$transcript);
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220
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221 $transcript->temporary_id($contig->id . "." . $endphase);
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222
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223 my $count = 1;
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224 my @exons;
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225
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226
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227 foreach my $f (@f) {
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228 #print "exon seqname = ".$f->seqname."\n";
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229 my $exon = new Bio::EnsEMBL::Exon;
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230 #print STDERR "exon ".$f->gffstring."\n";
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231 push(@exons,$exon);
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232 $exon->seqname($f->seqname);
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233 $exon->temporary_id ($contig->id . ".$count");
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234 $exon->contig ($contig);
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235 $exon->start ($f->start);
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236 $exon->end ($f->end );
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237 $exon->strand ($f->strand);
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238 $exon->slice($contig);
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239 $exon->phase ($endphase);
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240 $exon->end_phase( ($exon->phase + $exon->length)%3 );
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241 #$exon->score ($f->score);
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242 # $exon->p_value ($f->p_value);
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243 $endphase = $exon->end_phase;
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244
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245 $transcript->add_Exon($exon);
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246 $count++;
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247
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248 #print STDERR "Added exon start " . $exon->start . " end " . $exon->end . " strand " . $exon->strand . " score " . $exon->score . " pvalue " . $exon->p_value . "\n";
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249 }
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250
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251 my $translation = new Bio::EnsEMBL::Translation;
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252
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253 my $contig_id = "";
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254 my $fset_id = "";
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255
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256 if (defined($contig->id)) {
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257 $contig_id = $contig->id;
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258 }
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259 if (defined($fset->id)) {
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260 $fset_id = $fset->id;
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261 }
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262
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263 $translation->temporary_id($contig_id . "." . $fset_id);
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264 $translation->start (1);
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265 $translation->end ($exons[$#exons]->end - $exons[$#exons]->start + 1);
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266 $translation->start_Exon($exons[0]);
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267 $translation->end_Exon ($exons[$#exons]);
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268 $transcript->translation($translation);
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269
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270 # print STDERR "Phase $startphase " . $transcript->translate->seq . "\n";
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271
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272 $startphase++;
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273 }
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274 #print "finshed fset2transcript_3frame\n";
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275 return @transcripts;
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276 }
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277
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278
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279 sub fset2transcript_with_seq {
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280 my ($genscan,$seq)=@_;
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281
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282
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283 unless ($genscan->isa ("Bio::EnsEMBL::SeqFeatureI"))
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284 {print "$genscan must be Bio::EnsEMBL::SeqFeatureI\n";}
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285 unless ($seq->isa ("Bio::PrimarySeqI") || $seq->isa ("Bio::SeqI"))
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286 {print "$seq must be Bio::SeqI or a Bio::PrimarySeqI\n";}
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287
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288 #print STDERR "running fset2transcript\n";
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289 my $transcript = new Bio::EnsEMBL::Transcript;
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290 $transcript->temporary_id($seq->id . "." . $genscan->seqname);
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291
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292 my @exons;
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293 my $count= 1;
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294
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295 foreach my $f ($genscan->sub_SeqFeature) {
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296
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297 my $exon = new Bio::EnsEMBL::Exon;
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298 $exon->contig ($seq);
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299 $exon->start ($f->start);
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300 $exon->end ($f->end );
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301 $exon->strand ($f->strand);
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302 $exon->phase ($f->phase);
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303 $exon->end_phase( ($exon->phase + $exon->length)%3 );
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304 #$exon->score ($f->score);
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305 #print STDERR "contig is a = ".$seq."\n";
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306 $exon->slice($seq);
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307
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308 push(@exons,$exon);
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309 $count++;
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310
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311 }
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312
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313 foreach my $exon (@exons) {
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314
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315 $transcript->add_Exon($exon);
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316
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317
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318 }
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319 return $transcript;
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320
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321 }
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322
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323
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324
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325 1;
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