annotate scripts/pickOverlapPair.ex.pl @ 18:e198b686bfe4 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit edf843bf10fa262f075980626a9201078f868757
author mvdbeek
date Wed, 17 Aug 2016 11:49:25 -0400
parents 28d1a6f8143f
children 9672fe07a232
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1 #!/share/bin/perl
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2 use Bio::Seq;
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3 use List::Util qw(sum);
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5 die "perl $0 <*.excision.cluster.rpmk.refined.bp>\n" if @ARGV<0;
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7 my $title=$ARGV[0];
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8 if ($title =~ /annotation/) {
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9 $title =~ s/excision.cluster.annotation.refined.bp/sorted.bam/;
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10 }
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11 else {$title =~ s/excision.cluster.rpmk.refined.bp/sorted.bam/;}
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12 #system("samtools index /home/wangj2/scratch/bill/bill_genomic/$title");
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13
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14 my %chrs=();
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15 system("samtools view -H $title > header");
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16 open (input, "<header") or die "Can't open header since $!\n";
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17 while (my $line=<input>) {
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18 if ($line =~ /^\@SQ/) {
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19 my @a=split(/\t/, $line);
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20 for my $j (0..$#a) {
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21 if ($a[$j] =~ /^SN:/) {
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22 $a[$j] =~ s/^SN://;
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23 $chrs{$a[$j]}=1;
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24 }
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25 }
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26 }
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27 }
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28 close input;
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29 system("rm header");
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31 open (input, "<$ARGV[0]") or die "Can't open $ARGV[0] since $!\n";
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32 my $header=<input>;
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33 while (my $line=<input>) {
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34 chomp($line);
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35 my @a=split(/\t/, $line);
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36
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37 my $left=0;
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38 my $right=0;
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39 if ($a[4] eq "") {$left=$a[1];}
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40 else {
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41 my @t=split(/\,/, $a[4]);
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42 my @p=split(/\(/, $t[$#t]);
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43 $left=$p[0];
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44 }
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45 if ($a[5] eq "") {$right=$a[2];}
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46 else {
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47 my @t=split(/\,/, $a[5]);
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48 my @p=split(/\(/, $t[0]);
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49 $right=$p[0];
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50 }
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51
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52 my $leftlower=$left-500;
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53 my $leftupper=$left+500;
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54 my $rightlower=$right-500;
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55 my $rightupper=$right+500;
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56 my $chr_num=$a[0];
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57 $chr_num =~ s/chr//;
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58 if (($chrs{$a[0]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[0];}
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59 system("samtools view -Xf 0x2 $title $chr_num\:$leftlower\-$leftupper $chr_num\:$rightlower\-$rightupper > temp.sam");
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60
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61 open in,"temp.sam";
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62 my %ps=();
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63 my %me=();
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64 my %uniqp=();
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65 my %uniqm=();
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66 my $ref_sup=0;
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67
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68 while(<in>)
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69 {
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70 chomp;
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71 my @f=split/\t/,$_,12;
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72 ## read number 1 or 2
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73 my ($rnum)=$f[1]=~/(\d)$/;
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74
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75 ## XT:A:*
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76 my ($xt)=$f[11]=~/XT:A:(.)/;
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77
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78 ## Coordinate
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79 my $coor=$f[3];
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80 if ($f[1]=~/r/)
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81 {
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82 if ($xt eq "U") {$uniqm{$f[0]}=1;}
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83 my (@cigar_m)=$f[5]=~/(\d+)M/g;
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84 my (@cigar_d)=$f[5]=~/(\d+)D/g;
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85 my (@cigar_s)=$f[5]=~/(\d+)S/g;
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86 my (@cigar_i)=$f[5]=~/(\d+)I/g;
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87 my $aln_ln=sum(@cigar_m,@cigar_d);
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88 $me{$f[0]}=$f[3]+$aln_ln-1;
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89 }
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90 elsif ($f[1]=~/R/) {
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91 $ps{$f[0]}=$f[3];
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92 if ($xt eq "U") {$uniqp{$f[0]}=1;}
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93 }
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94
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95 # ${$pe{$f[0]}}[$rnum-1]=[$xt,$coor];
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96 }
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97 close in;
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98
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99 foreach my $id (keys %ps)
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100 {
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101 # my @rid=@{$pe{$id}};
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102
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103 # if(($rid[0][0] eq "U" && $rid[1][0] eq "M") || ($rid[0][0] eq "M" && $rid[1][0] eq "U"))
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104 # {
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105 # $soft_clip++;
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106 # print "$id\n";
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107 # }
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108
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109 if ((defined $me{$id})&&((defined $uniqp{$id})||(defined $uniqm{$id})))
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110 {
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111 if (((($ps{$id}+5)<=$right)&&($me{$id}>$right)&&($uniqm{$id}==1)) || ((($me{$id}-5)>=$left)&&($ps{$id}<$left)&&($uniqp{$id}==1))) {
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112 $ref_sup++;
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113 }
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114 }
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115 }
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116
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117 print "$a[0]\t$a[1]\t$a[2]\t$a[3]\t$left\t$right\t$ref_sup\n";
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118 system("rm temp.sam");
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119 }
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120