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1 # BioPerl module for Bio::Tools::RepeatMasker
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2 #
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3 # Cared for by Shawn Hoon <shawnh@fugu-sg.org>
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4 #
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5 # Copyright Shawn Hoon
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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::RepeatMasker - DESCRIPTION of Object
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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::RepeatMasker;
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18 my $parser = new Bio::Tools::RepeatMasker(-file => 'seq.fa.out');
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19 while( my $result = $parser->next_result ) {
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20
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21 }
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22
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23 =head1 DESCRIPTION
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24
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25 A parser for RepeatMasker output
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26
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27 =head1 FEEDBACK
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28
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29 =head2 Mailing Lists
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30
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31 User feedback is an integral part of the evolution of this and other
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32 Bioperl modules. Send your comments and suggestions preferably to
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33 the Bioperl mailing list. Your participation is much appreciated.
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34
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35 bioperl-l@bioperl.org - General discussion
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36 http://bioperl.org/MailList.shtml - About the mailing lists
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37
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38 =head2 Reporting Bugs
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39
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40 Report bugs to the Bioperl bug tracking system to help us keep track
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41 of the bugs and their resolution. Bug reports can be submitted via
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42 email or the web:
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43
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44 bioperl-bugs@bioperl.org
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45 http://bugzilla.bioperl.org/
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46
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47 =head1 AUTHOR - Shawn Hoon
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48
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49 Email shawnh@fugu-sg.org
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50
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51 Describe contact details here
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52
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53 =head1 CONTRIBUTORS
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54
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55 Additional contributors names and emails here
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56
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57 =head1 APPENDIX
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58
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59 The rest of the documentation details each of the object methods.
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60 Internal methods are usually preceded with a _
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61
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62 =cut
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63
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64
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65 # Let the code begin...
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66
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67
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68 package Bio::Tools::RepeatMasker;
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69 use vars qw(@ISA);
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70 use strict;
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71
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72 use Bio::Root::Root;
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73 use Bio::SeqFeature::FeaturePair;
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74 use Bio::Root::IO;
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75
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76 @ISA = qw(Bio::Root::Root Bio::Root::IO );
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77
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78 =head2 new
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79
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80 Title : new
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81 Usage : my $obj = new Bio::Tools::RepeatMasker();
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82 Function: Builds a new Bio::Tools::RepeatMasker object
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83 Returns : Bio::Tools::RepeatMasker
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84 Args : -fh/-file => $val, # for initing input, see Bio::Root::IO
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85
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86
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87 =cut
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88
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89 sub new {
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90 my($class,@args) = @_;
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91
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92 my $self = $class->SUPER::new(@args);
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93 $self->_initialize_io(@args);
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94
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95 return $self;
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96 }
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97
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98 =head2 next_result
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99
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100 Title : next_result
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101 Usage : my $r = $rpt_masker->next_result
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102 Function: Get the next result set from parser data
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103 Returns : L<Bio::SeqFeature::FeaturePair>
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104 Args : none
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105
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106
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107 =cut
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108
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109 sub next_result{
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110 my ($self) = @_;
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111 while ($_=$self->_readline()) {
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112 if (/no repetitive sequences detected/) {
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113 print STDERR "RepeatMasker didn't find any repetitive sequences\n";
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114 return ;
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115 }
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116 if (/\d+/) { #ignore introductory lines
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117 my @element = split;
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118 # ignore features with negatives
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119 next if ($element[11-13] =~ /-/);
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120 my (%feat1, %feat2);
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121 my ($score, $query_name, $query_start, $query_end, $strand,
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122 $repeat_name, $repeat_class ) = (split)[0, 4, 5, 6, 8, 9, 10];
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123
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124 my ($hit_start,$hit_end);
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125 if ($strand eq '+') {
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126 ($hit_start, $hit_end) = (split)[11, 12];
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127 $strand = 1;
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128 }
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129 elsif ($strand eq 'C') {
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130 ($hit_start, $hit_end) = (split)[12, 13];
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131 $strand = -1;
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132 }
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133 my $rf = Bio::SeqFeature::Generic->new;
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134 $rf->seq_id ($query_name);
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135 $rf->score ($score);
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136 $rf->start ($query_start);
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137 $rf->end ($query_end);
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138 $rf->strand ($strand);
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139 $rf->source_tag ("RepeatMasker");
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140 $rf->primary_tag ($repeat_class);
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141 my $rf2 = Bio::SeqFeature::Generic->new;
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142 $rf2->seq_id ($repeat_name);
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143 $rf2->score ($score);
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144 $rf2->start ($hit_start);
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145 $rf2->end ($hit_end);
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146 $rf2->strand ($strand);
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147 $rf2->source_tag ("RepeatMasker");
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148 $rf->primary_tag ($repeat_class);
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149 my $fp = Bio::SeqFeature::FeaturePair->new(-feature1=>$rf,
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150 -feature2=>$rf2);
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151
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152 return $fp;
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153 }
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154 }
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155 }
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156
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157 1;
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