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1 # $Id: Grail.pm,v 1.6 2002/12/01 00:05:21 jason Exp $
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2 #
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3 # BioPerl module for Bio::Tools::Grail
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Tools::Grail - Results of one Grail run
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16
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17 =head1 SYNOPSIS
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18
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19 $grail = Bio::Tools::Grail->new(-file => 'result.grail');
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20 # filehandle:
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21 $grail = Bio::Tools::Grail->new( -fh => \*INPUT );
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22
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23 # parse the results
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24 while($gene = $grail->next_prediction()) {
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25 # $gene is an instance of Bio::Tools::Prediction::Gene
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26
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27 # $gene->exons() returns an array of
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28 # Bio::Tools::Prediction::Exon objects
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29 # all exons:
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30 @exon_arr = $gene->exons();
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31
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32 # initial exons only
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33 @init_exons = $gene->exons('Initial');
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34 # internal exons only
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35 @intrl_exons = $gene->exons('Internal');
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36 # terminal exons only
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37 @term_exons = $gene->exons('Terminal');
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38 # singleton exons only -- should be same as $gene->exons() because
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39 # there are no other exons supposed to exist in this structure
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40 @single_exons = $gene->exons('Single');
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41 }
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42
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43 # essential if you gave a filename at initialization (otherwise the file
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44 # will stay open)
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45 $genscan->close();
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46
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47 =head1 DESCRIPTION
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48
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49 The Grail module provides a parser for Grail gene structure prediction
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50 output.
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51
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52
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53 =head1 FEEDBACK
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54
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55 =head2 Mailing Lists
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56
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57 User feedback is an integral part of the evolution of this and other
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58 Bioperl modules. Send your comments and suggestions preferably to one
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59 of the Bioperl mailing lists. Your participation is much appreciated.
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60
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61 bioperl-l@bioperl.org - General discussion
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62 http://bio.perl.org/MailList.html - About the mailing lists
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63
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64 =head2 Reporting Bugs
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65
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66 Report bugs to the Bioperl bug tracking system to help us keep track
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67 the bugs and their resolution. Bug reports can be submitted via email
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68 or the web:
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69
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70 bioperl-bugs@bio.perl.org
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71 http://bugzilla.bioperl.org/
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72
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73 =head1 AUTHOR - Jason Stajich
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74
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75 Email jason@bioperl.org
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76
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77 Describe contact details here
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78
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79 =head1 APPENDIX
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80
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81 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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82
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83 =cut
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84
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85 # Let the code begin...
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86
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87 package Bio::Tools::Grail;
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88 use vars qw(@ISA);
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89 use strict;
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90
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91 use Bio::Root::Root;
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92 use Bio::Root::IO;
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93 use Bio::Tools::Prediction::Gene;
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94 use Bio::Tools::Prediction::Exon;
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95 use Symbol;
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96
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97 @ISA = qw(Bio::Root::IO Bio::Root::Root);
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98
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99 sub new {
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100 my($class,@args) = @_;
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101
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102 my $self = $class->SUPER::new(@args);
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103 $self->_initialize_io(@args);
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104
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105 return $self;
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106 }
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107
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108 =head2 next_prediction
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109
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110 Title : next_prediction
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111 Usage : while($gene = $grail->next_prediction()) {
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112 # do something
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113 }
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114 Function: Returns the next gene structure prediction of the Grail result
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115 file. Call this method repeatedly until FALSE is returned.
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116
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117 Example :
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118 Returns : A Bio::Tools::Prediction::Gene object.
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119 Args :
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120
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121 =cut
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122
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123 sub next_prediction {
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124 my ($self) = @_;
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125
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126 # get next gene structure
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127 my $gene = $self->_prediction();
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128
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129 if($gene) {
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130 # fill in predicted protein, and if available the predicted CDS
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131 #
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132 my ($id, $seq);
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133 # use the seq stack if there's a seq on it
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134 my $seqobj = pop(@{$self->{'_seqstack'}});
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135 if(! $seqobj) {
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136 # otherwise read from input stream
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137 ($id, $seq) = $self->_read_fasta_seq();
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138 $seqobj = Bio::PrimarySeq->new('-seq' => $seq,
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139 '-display_id' => $id,
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140 '-alphabet' => "protein");
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141 }
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142 # check that prediction number matches the prediction number
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143 # indicated in the sequence id (there may be incomplete gene
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144 # predictions that contain only signals with no associated protein
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145 # and CDS, like promoters, poly-A sites etc)
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146 $gene->primary_tag() =~ /[^0-9]([0-9]+)$/;
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147 my $prednr = $1;
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148 if($seqobj->display_id() !~ /_predicted_\w+_$prednr\|/) {
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149 # this is not our sequence, so push back for the next prediction
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150 push(@{$self->{'_seqstack'}}, $seqobj);
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151 } else {
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152 $gene->predicted_protein($seqobj);
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153 # CDS prediction, too?
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154 if($self->_has_cds()) {
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155 ($id, $seq) = $self->_read_fasta_seq();
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156 $seqobj = Bio::PrimarySeq->new('-seq' => $seq,
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157 '-display_id' => $id,
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158 '-alphabet' => "dna");
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159 $gene->predicted_cds($seqobj);
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160 }
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161 }
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162 }
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163 return $gene;
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164 }
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165
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166 =head2 _parse_predictions
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167
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168 Title : _parse_predictions()
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169 Usage : $obj->_parse_predictions()
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170 Function: Parses the prediction section. Automatically called by
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171 next_prediction() if not yet done.
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172 Example :
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173 Returns :
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174
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175 =cut
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176
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177 sub _parse_predictions {
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178 my ($self) = @_;
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179
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180 # code needs to go here
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181
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182 $self->_predictions_parsed(1);
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183 }
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184
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185 =head2 _prediction
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186
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187 Title : _prediction()
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188 Usage : $gene = $obj->_prediction()
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189 Function: internal
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190 Example :
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191 Returns :
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192
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193 =cut
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194
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195 sub _prediction {
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196 my ($self) = @_;
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197
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198 return undef unless(exists($self->{'_preds'}) && @{$self->{'_preds'}});
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199 return shift(@{$self->{'_preds'}});
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200 }
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201
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202 =head2 _add_prediction
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203
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204 Title : _add_prediction()
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205 Usage : $obj->_add_prediction($gene)
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206 Function: internal
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207 Example :
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208 Returns :
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209
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210 =cut
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211
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212 sub _add_prediction {
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213 my ($self, $gene) = @_;
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214
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215 if(! exists($self->{'_preds'})) {
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216 $self->{'_preds'} = [];
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217 }
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218 push(@{$self->{'_preds'}}, $gene);
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219 }
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220
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221 =head2 _predictions_parsed
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222
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223 Title : _predictions_parsed
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224 Usage : $obj->_predictions_parsed
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225 Function: internal
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226 Example :
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227 Returns : TRUE or FALSE
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228
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229 =cut
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230
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231 sub _predictions_parsed {
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232 my ($self, $val) = @_;
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233
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234 $self->{'_preds_parsed'} = $val if $val;
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235 if(! exists($self->{'_preds_parsed'})) {
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236 $self->{'_preds_parsed'} = 0;
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237 }
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238 return $self->{'_preds_parsed'};
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239 }
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240
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241 =head2 _has_cds
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242
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243 Title : _has_cds()
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244 Usage : $obj->_has_cds()
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245 Function: Whether or not the result contains the predicted CDSs, too.
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246 Example :
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247 Returns : TRUE or FALSE
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248
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249 =cut
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250
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251 sub _has_cds {
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252 my ($self, $val) = @_;
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253
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254 $self->{'_has_cds'} = $val if $val;
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255 if(! exists($self->{'_has_cds'})) {
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256 $self->{'_has_cds'} = 0;
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257 }
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258 return $self->{'_has_cds'};
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259 }
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260
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261 1;
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