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1 # $Id: Genomewise.pm,v 1.1.2.1 2003/03/25 12:32:16 heikki Exp $
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2 #
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3 # BioPerl module for Bio::Tools::Genomewise
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4 #
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5 # Copyright Jason Stajich <jason@bioperl.org>
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6 #
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7 # You may distribute this module under the same terms as perl itself
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8 #
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9 # POD documentation - main docs before the code
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10
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11 =head1 NAME
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12
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13 Bio::Tools::Genomewise - Results of one Genomewise run
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14
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15 =head1 SYNOPSIS
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16
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17 use Bio::Tools::Genomewise;
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18 my $gw = Bio::Tools::Genomewise(-file=>"genomewise.out");
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19
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20 while (my $gene = $gw->next_prediction){
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21 my @transcripts = $gw->transcripts;
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22 foreach my $t(@transcripts){
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23 my @exons = $t->exons;
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24 foreach my $e(@exons){
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25 print $e->start." ".$e->end."\n";
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26 }
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27 }
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28 }
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29
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30 =head1 DESCRIPTION
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31
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32 This is the parser for the output of Genewise. It takes either a file
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33 handle or a file name and returns a
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34 Bio::SeqFeature::Gene::GeneStructure object. You will need to specify
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35 the proper target sequence id on the object with the
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36 $feature-E<gt>seq_id($seqid).
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37
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38 =head1 FEEDBACK
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39
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40 =head2 Mailing Lists
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41
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42 User feedback is an integral part of the evolution of this and other
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43 Bioperl modules. Send your comments and suggestions preferably to one
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44 of the Bioperl mailing lists. Your participation is much appreciated.
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45
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46 bioperl-l@bioperl.org - General discussion
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47 http://bio.perl.org/MailList.html - About the mailing lists
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48
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49 =head2 Reporting Bugs
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50
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51 Report bugs to the Bioperl bug tracking system to help us keep track
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52 the bugs and their resolution. Bug reports can be submitted via email
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53 or the web:
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54
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55 bioperl-bugs@bio.perl.org
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56 http://bugzilla.bioperl.org/
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57
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58 =head1 AUTHOR - Fugu Team
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59
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60 Email: fugui@worf.fugu-sg.org
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61
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62 =head1 APPENDIX
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63
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64 The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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65
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66 =cut
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67
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68
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69 # Let the code begin...
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70
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71
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72 package Bio::Tools::Genomewise;
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73 use vars qw(@ISA $Srctag);
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74 use strict;
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75
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76 use Bio::Tools::Genewise;
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77 use Bio::Tools::AnalysisResult;
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78 use Bio::SeqFeature::Generic;
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79 use Bio::SeqFeature::Gene::Exon;
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80 use Bio::SeqFeature::FeaturePair;
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81 use Bio::SeqFeature::Gene::Transcript;
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82 use Bio::SeqFeature::Gene::GeneStructure;
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83
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84 @ISA = qw(Bio::Tools::Genewise);
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85
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86 $Srctag = 'genomewise';
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87
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88 =head2 new
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89
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90 Title : new
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91 Usage : $obj->new(-file=>"genewise.out");
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92 $obj->new(-fh=>\*GW);
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93 Function: Constructor for genomewise wrapper. Takes either a file or filehandle
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94 Example :
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95 Returns : L<Bio::Tools::Genomewise>
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96
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97 =cut
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98
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99 sub new {
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100 my($class,@args) = @_;
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101 my $self = $class->SUPER::new(@args);
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102 return $self;
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103 }
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104
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105 =head2 _get_strand
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106
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107 Title : _get_strand
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108 Usage : $obj->_get_strand
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109 Function: takes start and end values, swap them if start>end and returns end
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110 Example :
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111 Returns :$start,$end,$strand
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112
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113 =cut
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114
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115 =head2 score
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116
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117 Title : score
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118 Usage : $obj->score
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119 Function: get/set for score info
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120 Example :
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121 Returns : a score value
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122
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123 =cut
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124
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125 =head2 _prot_id
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126
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127 Title : _prot_id
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128 Usage : $obj->_prot_id
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129 Function: get/set for protein id
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130 Example :
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131 Returns :a protein id
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132
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133 =cut
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134
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135 =head2 _target_id
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136
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137 Title : _target_id
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138 Usage : $obj->_target_id
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139 Function: get/set for genomic sequence id
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140 Example :
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141 Returns :a target id
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142
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143 =cut
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144
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145
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146 =head2 next_prediction
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147
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148 Title : next_prediction
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149 Usage : while($gene = $genewise->next_prediction()) {
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150 # do something
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151 }
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152 Function: Returns the gene structure prediction of the Genomewise result
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153 file. Call this method repeatedly until FALSE is returned.
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154
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155 Example :
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156 Returns : a Bio::SeqFeature::Gene::GeneStructure object
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157 Args :
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158
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159 =cut
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160
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161
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162 sub next_prediction {
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163 my ($self) = @_;
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164
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165 my $genes;
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166 while ($_ = $self->_readline) {
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167 $self->debug( $_ ) if( $self->verbose > 0);
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168 last if( /^\/\//);
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169
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170 if( /^Gene\s+\d+\s*$/ ) {
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171 $genes = new Bio::SeqFeature::Gene::GeneStructure
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172 (-source => $Srctag,
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173 -seq_id => $self->_target_id, # if this had been specified
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174 );
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175 $_ = $self->_readline;
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176 $self->debug( $_ ) if( $self->verbose > 0);
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177
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178 unless ( /^Gene\s+(\d+)\s+(\d+)\s*$/ ) {
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179 $self->warn("Unparseable genomewise output");
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180 last;
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181 }
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182 my $transcript = new Bio::SeqFeature::Gene::Transcript
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183 (-source => $Srctag,
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184 -seq_id => $self->_target_id, # if this had been specified
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185 -start => $1,
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186 -end => $2,
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187 );
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188 my $nbr = 1;
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189 while( $_ = $self->_readline ) {
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190 $self->debug( $_ ) if( $self->verbose > 0);
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191
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192 unless( m/^\s+Exon\s+(\d+)\s+(\d+)\s+phase\s+(\d+)/ ){
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193 $self->_pushback($_);
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194 last;
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195 }
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196 my ($e_start,$e_end,$phase,$e_strand) = ($1,$2,$3);
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197
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198 ($e_start,$e_end,$e_strand) = $self->_get_strand($e_start,
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199 $e_end);
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200 $transcript->strand($e_strand) unless $transcript->strand != 0;
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201
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202 my $exon = new Bio::SeqFeature::Gene::Exon
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203 (-seq_id=>$self->_target_id,
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204 -source => $Srctag,
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205 -start=>$e_start,
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206 -end=>$e_end,
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207 -frame => $phase,
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208 -strand=>$e_strand);
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209 $exon->add_tag_value("Exon",$nbr++);
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210 $exon->add_tag_value('phase',$phase);
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211 $transcript->add_exon($exon);
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212 }
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213 $genes->add_transcript($transcript);
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214 last; # only process a single gene at a time
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215 }
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216 }
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217 return $genes;
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218 }
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219 1;
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