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1 package LevD;
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2
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3 use lib "/data2/bsi/reference/softsearch/lib/perl5";
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4 use strict;
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5 use warnings;
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6 use Data::Dumper;
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7 use String::Approx 'adist';
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8 use String::Approx 'adistr';
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9 use String::Approx 'aindex';
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10
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11 my $WINDOW_SIZE = 100;
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12
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13 sub new {
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14 my ($class, $file) = @_;
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15 my $self = {};
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16
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17 bless($self,$class);
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18 $self->init();
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19
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20 return $self;
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21 }
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22
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23 sub init {
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24 my ($self) = @_;
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25
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26 #### default values.
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27 $self->{index} = 0;
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28 $self->{relative_edit_dist} = 0;
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29 $self->{edit_dist} = 0;
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30 }
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31
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32 sub search {
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33 my ($self, $clip, $chr, $start, $stop, $ref) = @_;
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34
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35 if (! -s $ref) {
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36 die "ERROR: Reference file $ref now found\n";
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37 }
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38
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39 #### extact seq from reference file.
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40 my $target = $chr .":". $start ."-". $stop;
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41 my $cmd = "samtools faidx $ref $target";
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42
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43 my @output = $self->_run_system_cmd($cmd);
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44
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45 #### depending on ref file format seq could be on multiple lines
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46 #### concatinate all except for the header in one line.
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47 #### e.g:
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48 #### >chr1:8222999-8223099
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49 #### GGTGCAATCATAGCTCACTAAGCTTCAACCTCAAGAGATCCTCCCACCTCAGCCTCCCAG
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50 #### GTAGCTGGGACTACAGGCAAATGCCATGACACCTAGCTAAT
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51 my $seq = join("", @output[1..$#output]);
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52
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53 #### remove new line character
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54 $seq =~ s/\n//g;
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55
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56 #### find number of mismatches and start index
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57 #### of clip to be searched against target seq.
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58 $self->{relative_edit_dist} = adistr($clip, $seq);
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59 $self->{edit_dist} = adist($clip, $seq);
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60 $self->{index} = aindex($clip, $seq);
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61 }
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62
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63 sub _run_system_cmd {
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64 my ($self, $cmd) = @_;
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65 my @cmd_output;
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66
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67 eval {
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68 @cmd_output = qx{$cmd 2>&1};
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69 if ( ($? << 8) != 0 ) {
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70 die "@cmd_output";
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71 }
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72 };
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73 if ($@) {
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74 die "Error executing command $cmd: $@";
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75 }
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76
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77 return @cmd_output;
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78 }
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79
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80 1;
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