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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: 0.1.5
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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 &wgsim_eval;
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11 exit;
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12
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13 sub wgsim_eval {
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14 my %opts = (g=>5);
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15 getopts('pcag:', \%opts);
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16 die("Usage: wgsim_eval.pl [-pca] [-g $opts{g}] <in.sam>\n") if (@ARGV == 0 && -t STDIN);
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17 my (@c0, @c1, %fnfp);
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18 my ($max_q, $flag) = (0, 0);
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19 my $gap = $opts{g};
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20 $flag |= 1 if (defined $opts{p});
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21 $flag |= 2 if (defined $opts{c});
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22 while (<>) {
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23 next if (/^\@/);
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24 my @t = split("\t");
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25 next if (@t < 11);
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26 my $line = $_;
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27 my ($q, $is_correct, $chr, $left, $rght) = (int($t[4]/10), 1, $t[2], $t[3], $t[3]);
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28 $max_q = $q if ($q > $max_q);
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29 # right coordinate
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30 $_ = $t[5]; s/(\d+)[MDN]/$rght+=$1,'x'/eg;
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31 --$rght;
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32 # correct for soft clipping
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33 my ($left0, $rght0) = ($left, $rght);
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34 $left -= $1 if (/^(\d+)[SH]/);
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35 $rght += $1 if (/(\d+)[SH]$/);
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36 $left0 -= $1 if (/(\d+)[SH]$/);
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37 $rght0 += $1 if (/^(\d+)[SH]/);
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38 # skip unmapped reads
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39 next if (($t[1]&0x4) || $chr eq '*');
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40 # parse read name and check
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41 if ($t[0] =~ /^(\S+)_(\d+)_(\d+)_/) {
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42 if ($1 ne $chr) { # different chr
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43 $is_correct = 0;
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44 } else {
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45 if ($flag & 2) {
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46 if (($t[1]&0x40) && !($t[1]&0x10)) { # F3, forward
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47 $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
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48 } elsif (($t[1]&0x40) && ($t[1]&0x10)) { # F3, reverse
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49 $is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap);
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50 } elsif (($t[1]&0x80) && !($t[1]&0x10)) { # R3, forward
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51 $is_correct = 0 if (abs($3 - $left) > $gap && abs($3 - $left0) > $gap);
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52 } else { # R3, reverse
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53 $is_correct = 0 if (abs($2 - $rght) > $gap && abs($3 - $rght0) > $gap);
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54 }
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55 } else {
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56 if ($t[1] & 0x10) { # reverse
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57 $is_correct = 0 if (abs($3 - $rght) > $gap && abs($3 - $rght0) > $gap); # in case of indels that are close to the end of a reads
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58 } else {
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59 $is_correct = 0 if (abs($2 - $left) > $gap && abs($2 - $left0) > $gap);
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60 }
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61 }
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62 }
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63 } else {
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64 warn("[wgsim_eval] read '$t[0]' was not generated by wgsim?\n");
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65 next;
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66 }
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67 ++$c0[$q];
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68 ++$c1[$q] unless ($is_correct);
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69 @{$fnfp{$t[4]}} = (0, 0) unless (defined $fnfp{$t[4]});
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70 ++$fnfp{$t[4]}[0];
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71 ++$fnfp{$t[4]}[1] unless ($is_correct);
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72 print STDERR $line if (($flag&1) && !$is_correct && $q > 0);
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73 }
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74 # print
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75 my ($cc0, $cc1) = (0, 0);
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76 if (!defined($opts{a})) {
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77 for (my $i = $max_q; $i >= 0; --$i) {
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78 $c0[$i] = 0 unless (defined $c0[$i]);
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79 $c1[$i] = 0 unless (defined $c1[$i]);
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80 $cc0 += $c0[$i]; $cc1 += $c1[$i];
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81 printf("%.2dx %12d / %-12d %12d %.3e\n", $i, $c1[$i], $c0[$i], $cc0, $cc1/$cc0) if ($cc0);
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82 }
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83 } else {
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84 for (reverse(sort {$a<=>$b} (keys %fnfp))) {
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85 next if ($_ == 0);
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86 $cc0 += $fnfp{$_}[0];
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87 $cc1 += $fnfp{$_}[1];
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88 print join("\t", $_, $cc0, $cc1), "\n";
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89 }
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90 }
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91 }
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