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1 #!/usr/bin/perl
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2
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3 use strict;
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4 use lib 'inc/perlmod';
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5 use ngsutil qw[ :DEFAULT &explode_varcall ];
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6 use warnings FATAL => qw[ numeric uninitialized ];
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7 use List::Util qw[ sum min max ];
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8 use File::Basename;
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9 use Getopt::Long;
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10
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11 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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12 # PATH TO YOUR R-bin DIRECTORY
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13 my $rbin = '/usr/bin/R';
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14 #!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
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15
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16 my $annovar_dir = 'inc/annovar';
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17 my $rdep = 'inc/R';
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18
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19 my($varfile, $outdir, $outfile, $i, @DP4, @buffer, @Temp, @previous, @fnames, %opts, %chr);
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20
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21 GetOptions(\%opts, "varfile=s", "outdir=s", "outfile=s");
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22 $varfile = $opts{varfile};
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23 $outdir = $opts{outdir};
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24 $outfile = $opts{outfile};
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25
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26 my $fname = readlink($varfile) || $varfile;
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27 $fname = basename($fname);
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28
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29 my %fh=(
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30 'chr1' => *chr1, 'chr2' => *chr2, 'chr3' => *chr3, 'chr4' => *chr4, 'chr5' => *chr5,
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31 'chr6' => *chr6, 'chr7' => *chr7, 'chr8' => *chr8, 'chr9' => *chr9, 'chr10' => *chr10,
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32 'chr11' => *chr11, 'chr12' => *chr12, 'chr13' => *chr13, 'chr14' => *chr14, 'chr15' => *chr15,
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33 'chr16' => *chr16, 'chr17' => *chr17, 'chr18' => *chr18, 'chr19' => *chr19, 'chr20' => *chr20,
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34 'chr21' => *chr21, 'chr22' => *chr22, 'chrX' => *chrX, 'chrY' => *chrY, 'chrM' => *chrM
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35 );
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36
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37 `${annovar_dir}/convert2annovar.pl -format vcf4 $varfile -includeinfo > ${outdir}/${fname}_Temp-00 2> /dev/null` and die $!;
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38
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39 open($fh{$_}, ">${outdir}/${fname}_${_}.Temp-00") or die $! foreach keys %fh;
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40 open IN, "<${outdir}/${fname}_Temp-00" or die $!;
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41 while(<IN>){
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42 /^(\S+)\s+(?:\S+\s+){2}(\S+)\s+(\S+)/;
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43 next if !exists $fh{$1};
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44 if(min(length($2), length($3))!=1){
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45 chomp;
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46 @buffer=split /\s+/, $_;
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47 @Temp=explode_varcall(@buffer[1,3..4]);
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48 for($i=0; $i<$#{$Temp[0]}; $i+=2){
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49 print{ $fh{$buffer[0]} } join("\t", $buffer[0], @{$Temp[0]}[$i..$i+1], @{$Temp[1]}[$i..$i+1], @buffer[6..$#buffer]), "\n";
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50 }
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51 next;
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52 }
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53 print{ $fh{$1} } $_;
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54 $chr{$1}++;
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55 }
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56 close IN;
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57 foreach (keys %fh){
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58 close($fh{$_});
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59 next if !exists $chr{$_};
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60 `sort -k2,2n -k3,3n ${outdir}/${fname}_${_}.Temp-00 > ${outdir}/${fname}_${_}.Temp-01` and die $!;
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61 open IN, "<${outdir}/${fname}_${_}.Temp-01" or die $!;
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62 open OUT, ">${outdir}/${fname}_${_}.Temp-02" or die $!;
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63 $_=readline(IN);
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64 /^((?:\S+\s+){7})(?:\S+\s+){8}(\S+\s+\S+)/;
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65 @buffer=split /\s+/, $1.$2;
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66 ($_=pop(@buffer))=~s/.+DP4=([^;]+).+/$1/;
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67 @DP4=split /,/, $_;
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68 push @buffer, @DP4;
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69 @previous=@buffer;
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70 MAINLOOP: while(<IN>){
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71 /^((?:\S+\s+){7})(?:\S+\s+){8}(\S+\s+\S+)/;
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72 @buffer=split /\s+/, $1.$2;
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73 ($_=pop(@buffer))=~s/.+DP4=([^;]+).+/$1/;
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74 @DP4=split /,/, $_;
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75 push @buffer, @DP4;
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76 while(($previous[0] eq $buffer[0]) && ($buffer[2]==$previous[2]+1) && (join('', @previous[3..4]) !~ /-/) && (join('', @buffer[3..4]) !~ /-/)){
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77 $previous[2]=$buffer[2];
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78 $previous[$_].=$buffer[$_] for 3..4;
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79 $previous[5]='unk' if $previous[5] ne $buffer[5];
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80 $previous[7]='SKIP' if $previous[7] ne $buffer[7];
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81 for (6,8..11){
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82 $previous[$_]+=$buffer[$_];
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83 $previous[$_]/=2;
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84 }
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85 next MAINLOOP;
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86 }
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87 $previous[7]='NONE' if $previous[7] eq '.';
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88 $previous[$_]=sprintf("%.0f", $previous[$_]) for (6,8..11);
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89 print OUT join("\t", @previous[0..6,8..11,7]), "\n";
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90 @Temp=@previous if eof;
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91 @previous=@buffer;
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92 }
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93 $previous[7]='NONE' if $previous[7] eq '.';
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94 $previous[$_]=sprintf("%.0f", $previous[$_]) for (6,8..11);
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95 print OUT join("\t", @previous[0..6,8..11,7]), "\n" if(join('_', @Temp[1..2]) ne join('_', @previous[1..2]));
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96 close IN;
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97 close OUT;
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98 }
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99 foreach (1..22, 'X', 'Y', 'M'){
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100 push @fnames, "${outdir}/${fname}_chr${_}.Temp-02" if exists $chr{"chr$_"};
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101 }
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102 system join(' ', 'cat', @fnames, '>', "${outdir}/${fname}.Temp.2R") and die $!;
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103 `${rbin} --vanilla --slave --args ${outdir}/${fname}.Temp.2R < ${rdep}/samvcf_data_parser.R` and die $!;
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104 system "rm ${outdir}/${fname}*Temp* $outfile; ln -s ${outdir}/${fname}.var $outfile" and die $!; |
