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1 #!/usr/bin/perl -w
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2
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3 # Contact: lh3
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4 # Version: 0.1.0
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5
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6 use strict;
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7 use warnings;
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8 use Getopt::Std;
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9
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10 &zoom2sam;
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11 exit;
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12
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13 sub mating {
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14 my ($s1, $s2) = @_;
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15 my $isize = 0;
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16 if ($s1->[2] ne '*' && $s1->[2] eq $s2->[2]) { # then calculate $isize
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17 my $x1 = ($s1->[1] & 0x10)? $s1->[3] + length($s1->[9]) : $s1->[3];
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18 my $x2 = ($s2->[1] & 0x10)? $s2->[3] + length($s2->[9]) : $s2->[3];
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19 $isize = $x2 - $x1;
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20 }
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21 # update mate coordinate
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22 if ($s2->[2] ne '*') {
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23 @$s1[6..8] = (($s2->[2] eq $s1->[2])? "=" : $s2->[2], $s2->[3], $isize);
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24 $s1->[1] |= 0x20 if ($s2->[1] & 0x10);
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25 } else {
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26 $s1->[1] |= 0x8;
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27 }
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28 if ($s1->[2] ne '*') {
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29 @$s2[6..8] = (($s1->[2] eq $s2->[2])? "=" : $s1->[2], $s1->[3], -$isize);
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30 $s2->[1] |= 0x20 if ($s1->[1] & 0x10);
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31 } else {
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32 $s2->[1] |= 0x8;
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33 }
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34 }
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35
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36 sub zoom2sam {
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37 my %opts = ();
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38 getopts("p", \%opts);
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39 die("Usage: zoom2sam.pl [-p] <readLen> <aln.zoom>
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40 Warnings: This script only supports the default Illumina outputs.\n") if (@ARGV < 2);
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41 my $is_paired = defined($opts{p});
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42 my $len = shift(@ARGV);
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43 # core loop
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44 my @s1 = ();
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45 my @s2 = ();
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46 my ($s_last, $s_curr) = (\@s1, \@s2);
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47 while (<>) {
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48 &zoom2sam_aux($_, $s_curr, $is_paired, $len);
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49 if (@$s_last != 0 && $s_last->[0] eq $s_curr->[0]) {
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50 &mating($s_last, $s_curr);
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51 print join("\t", @$s_last), "\n";
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52 print join("\t", @$s_curr), "\n";
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53 @$s_last = (); @$s_curr = ();
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54 } else {
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55 print join("\t", @$s_last), "\n" if (@$s_last != 0);
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56 my $s = $s_last; $s_last = $s_curr; $s_curr = $s;
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57 }
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58 }
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59 print join("\t", @$s_last), "\n" if (@$s_last != 0);
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60 }
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61
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62 sub zoom2sam_aux {
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63 my ($line, $s, $is_paired, $len) = @_;
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64 chomp($line);
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65 my @t = split("\t", $line);
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66 @$s = ();
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67 # read name
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68 $s->[0] = $t[0];
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69 # initial flag (will be updated later)
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70 $s->[1] = 0;
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71 $s->[1] |= 1 | 1<<6 if ($s->[0] =~ /_F$/);
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72 $s->[1] |= 1 | 1<<7 if ($s->[0] =~ /_R$/);
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73 $s->[1] |= 2 if ($is_paired);
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74 # read & quality
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75 $s->[9] = "*"; $s->[10] = "*";
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76 # cigar
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77 $s->[5] = $len . "M";
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78 # coor
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79 my @s = split(/\s+/, $t[1]);
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80 $s->[2] = $s[0];
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81 $t[1] =~ /:(\d+)$/;
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82 $s->[3] = $1 + 1;
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83 if ($s->[0] =~ /_[FR]$/) {
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84 my $u = ($s->[0] =~ /_F$/)? 1 : 0;
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85 my $w = ($t[2] eq '+')? 1 : 0;
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86 $s->[1] |= 0x10 if ($u ^ $w);
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87 $s->[0] =~ s/_[FR]$//;
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88 } else {
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89 $s->[1] |= 0x10 if ($t[2] eq '-');
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90 }
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91 # mapQ
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92 $s->[4] = 30;
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93 # mate coordinate
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94 $s->[6] = '*'; $s->[7] = $s->[8] = 0;
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95 # aux
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96 push(@$s, "NM:i:$t[3]");
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97 }
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