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1 # $Id: Utils.pm,v 1.1.2.1 2003/02/20 05:11:45 heikki Exp $
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2 #
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3 # BioPerl module for Bio::Coordinate::Utils
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4 #
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5 # Cared for by Heikki Lehvaslaiho <heikki@ebi.ac.uk>
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6 #
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7 # Copyright Heikki Lehvaslaiho
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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::Coordinate::Utils - Additional methods to create Bio::Coordinate objects
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16
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17 =head1 SYNOPSIS
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18
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19 use Bio::Coordinate::Utils;
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20 # get a Bio::Align::AlignI compliant object, $aln, somehow
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21 # it could be a Bio::SimpleAlign
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22
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23 $mapper = Bio::Coordinate::Utils->from_align($aln, 1);
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24
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25 =head1 DESCRIPTION
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26
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27 This class is a holder of methods that work on or create
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28 Bio::Coordinate::MapperI- compliant objects. . These methods are not
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29 part of the Bio::Coordinate::MapperI interface and should in general
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30 not be essential to the primary function of sequence objects. If you
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31 are thinking of adding essential functions, it might be better to
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32 create your own sequence class. See L<Bio::PrimarySeqI>,
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33 L<Bio::PrimarySeq>, and L<Bio::Seq> for more.
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34
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35 =head1 FEEDBACK
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36
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37 =head2 Mailing Lists
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38
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39 User feedback is an integral part of the evolution of this and other
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40 Bioperl modules. Send your comments and suggestions preferably to one
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41 of the Bioperl mailing lists. Your participation is much appreciated.
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42
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43 bioperl-l@bioperl.org - General discussion
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44 http://bio.perl.org/MailList.html - About the mailing lists
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45
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46 =head2 Reporting Bugs
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47
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48 Report bugs to the Bioperl bug tracking system to help us keep track
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49 the bugs and their resolution. Bug reports can be submitted via email
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50 or the web:
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51
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52 bioperl-bugs@bio.perl.org
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53 http://bugzilla.bioperl.org/
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54
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55 =head1 AUTHOR - Heikki Lehvaslaiho
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56
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57 Email: heikki@ebi.ac.uk
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58 Address:
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59
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60 EMBL Outstation, European Bioinformatics Institute
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61 Wellcome Trust Genome Campus, Hinxton
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62 Cambs. CB10 1SD, United Kingdom
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63
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64 =head1 APPENDIX
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65
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66 The rest of the documentation details each of the object
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67 methods. Internal methods are usually preceded with a _
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68
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69 =cut
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70
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71
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72 # Let the code begin...
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73
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74
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75 package Bio::Coordinate::Utils;
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76 use vars qw(@ISA);
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77
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78 use Bio::Location::Simple;
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79 use Bio::Coordinate::Pair;
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80 use Bio::Coordinate::Collection;
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81
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82 use strict;
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83
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84 @ISA = qw(Bio::Root::Root);
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85 # new inherited from Root
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86
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87 =head2 from_align
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88
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89 Title : from_align
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90 Usage : $mapper = Bio::Coordinate::Utils->from_align($aln, 1);
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91 Function:
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92 Create a mapper out of an alignment.
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93 The mapper will return a value only when both ends of
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94 the input range find a match.
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95
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96 Note: This implementation works only on pairwise alignments
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97 and is not yet well tested!
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98
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99 Returns : A Bio::Coordinate::MapperI
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100 Args : Bio::Align::AlignI object
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101 Id for the reference sequence, optional
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102
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103 =cut
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104
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105 sub from_align {
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106 my ($self, $aln, $ref ) = @_;
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107
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108 $aln->isa('Bio::Align::AlignI') ||
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109 $self->throw('Not a Bio::Align::AlignI object but ['. ref($self). ']');
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110
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111 # default reference sequence to the first sequence
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112 $ref ||= 1;
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113
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114 my $collection = Bio::Coordinate::Collection->new(-return_match=>1);
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115
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116 # this works only for pairs, so split the MSA
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117 # take the ref
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118 #foreach remaining seq in aln, do:
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119
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120 my $cs = $aln->consensus_string(49);
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121 while ( $cs =~ /([^-]+)/g) {
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122
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123 # alignment coordinates
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124 my $start = pos($cs) - length($1) + 1;
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125 my $end = $start+length($1)-1;
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126
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127 my $seq1 = $aln->get_seq_by_pos(1);
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128 my $seq2 = $aln->get_seq_by_pos(2);
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129
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130 my $match1 = Bio::Location::Simple->new
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131 (-seq_id => $seq1->id,
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132 -start => $seq1->location_from_column($start)->start,
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133 -end => $seq1->location_from_column($end)->start,
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134 -strand => $seq1->strand );
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135
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136 my $match2 = Bio::Location::Simple->new
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137 (-seq_id => $seq2->id,
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138 -start => $seq2->location_from_column($start)->start,
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139 -end => $seq2->location_from_column($end)->start,
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140 -strand => $seq2->strand );
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141
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142 my $pair = Bio::Coordinate::Pair->
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143 new(-in => $match1,
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144 -out => $match2
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145 );
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146
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147 $collection->add_mapper($pair);
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148 }
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149
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150 return @{$collection->each_mapper}[0] if $collection->each_mapper == 1;
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151 return $collection;
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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
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157 1;
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