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1 # $Id: selex.pm,v 1.10 2002/10/22 07:38:26 lapp Exp $
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2 #
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3 # BioPerl module for Bio::AlignIO::selex
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4
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5 # based on the Bio::SeqIO::selex module
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6 # by Ewan Birney <birney@sanger.ac.uk>
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7 # and Lincoln Stein <lstein@cshl.org>
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8 #
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9 # and the SimpleAlign.pm module of Ewan Birney
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10 #
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11 # Copyright Peter Schattner
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12 #
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13 # You may distribute this module under the same terms as perl itself
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14 # _history
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15 # September 5, 2000
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16 # POD documentation - main docs before the code
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17
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18 =head1 NAME
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19
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20 Bio::AlignIO::selex - selex sequence input/output stream
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21
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22 =head1 SYNOPSIS
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23
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24 Do not use this module directly. Use it via the L<Bio::AlignIO> class.
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25
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26 =head1 DESCRIPTION
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27
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28 This object can transform L<Bio::Align::AlignI> objects to and from selex flat
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29 file databases.
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30
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31 =head1 FEEDBACK
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32
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33 =head2 Reporting Bugs
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34
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35 Report bugs to the Bioperl bug tracking system to help us keep track
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36 the bugs and their resolution.
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37 Bug reports can be submitted via email or the web:
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38
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39 bioperl-bugs@bio.perl.org
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40 http://bugzilla.bioperl.org/
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41
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42 =head1 AUTHORS - Peter Schattner
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43
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44 Email: schattner@alum.mit.edu
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45
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46
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47 =head1 APPENDIX
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48
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49 The rest of the documentation details each of the object
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50 methods. Internal methods are usually preceded with a _
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51
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52 =cut
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53
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54 # Let the code begin...
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55
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56 package Bio::AlignIO::selex;
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57 use vars qw(@ISA);
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58 use strict;
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59 use Bio::AlignIO;
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60
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61 @ISA = qw(Bio::AlignIO);
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62
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63 =head2 next_aln
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64
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65 Title : next_aln
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66 Usage : $aln = $stream->next_aln()
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67 Function: returns the next alignment in the stream. Tries to read *all* selex
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68 It reads all non whitespace characters in the alignment
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69 area. For selexs with weird gaps (eg ~~~) map them by using
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70 $al->map_chars('~','-')
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71 Returns : L<Bio::Align::AlignI> object
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72 Args : NONE
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73
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74 =cut
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75
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76 sub next_aln {
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77 my $self = shift;
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78 my $entry;
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79 my ($start,$end,%align,$name,$seqname,$seq,$count,%hash,%c2name, %accession, $no);
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80 my $aln = Bio::SimpleAlign->new(-source => 'selex');
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81
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82 # in selex format, every non-blank line that does not start
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83 # with '#=' is an alignment segment; the '#=' lines are mark up lines.
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84 # Of particular interest are the '#=GF <name/st-ed> AC <accession>'
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85 # lines, which give accession numbers for each segment
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86
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87 while( $entry = $self->_readline) {
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88 $entry =~ /^\#=GS\s+(\S+)\s+AC\s+(\S+)/ && do {
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89 $accession{ $1 } = $2;
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90 next;
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91 };
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92 $entry !~ /^([^\#]\S+)\s+([A-Za-z\.\-]+)\s*/ && next;
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93
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94 $name = $1;
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95 $seq = $2;
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96
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97 if( ! defined $align{$name} ) {
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98 $count++;
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99 $c2name{$count} = $name;
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100 }
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101 $align{$name} .= $seq;
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102 }
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103
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104 # ok... now we can make the sequences
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105
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106 $count = 0;
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107 foreach $no ( sort { $a <=> $b } keys %c2name ) {
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108 $name = $c2name{$no};
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109
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110 if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) {
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111 $seqname = $1;
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112 $start = $2;
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113 $end = $3;
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114 } else {
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115 $seqname=$name;
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116 $start = 1;
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117 $end = length($align{$name});
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118 }
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119 $seq = new Bio::LocatableSeq('-seq'=>$align{$name},
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120 '-id'=>$seqname,
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121 '-start'=>$start,
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122 '-end'=>$end,
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123 '-type'=>'aligned',
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124 '-accession_number' => $accession{$name},
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125
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126 );
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127
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128 $aln->add_seq($seq);
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129 $count++;
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130 }
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131
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132 # If $end <= 0, we have either reached the end of
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133 # file in <> or we have encountered some other error
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134 #
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135 if ($end <= 0) { undef $aln;}
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136
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137 return $aln;
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138 }
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139
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140
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141 =head2 write_aln
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142
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143 Title : write_aln
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144 Usage : $stream->write_aln(@aln)
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145 Function: writes the $aln object into the stream in selex format
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146 Returns : 1 for success and 0 for error
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147 Args : L<Bio::Align::AlignI> object
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148
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149
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150 =cut
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151
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152 sub write_aln {
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153 my ($self,@aln) = @_;
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154 my ($namestr,$seq,$add);
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155 my ($maxn);
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156 foreach my $aln (@aln) {
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157 $maxn = $aln->maxdisplayname_length();
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158 foreach $seq ( $aln->each_seq() ) {
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159 $namestr = $aln->displayname($seq->get_nse());
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160 $add = $maxn - length($namestr) + 2;
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161 $namestr .= " " x $add;
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162 $self->_print (sprintf("%s %s\n",$namestr,$seq->seq())) or return;
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163 }
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164 }
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165 $self->flush if $self->_flush_on_write && defined $self->_fh;
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166 return 1;
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167 }
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168
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169 1;
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