annotate scripts/pickOverlapPair.in.pl @ 15:65ae84fc6689 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 7e0a7a19ee51f12bdcdfe84f3de67530a8990de9
author portiahollyoak
date Mon, 23 May 2016 10:37:52 -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 <input.insertion.refined.bp> <fragment size>\n" if @ARGV<1;
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7 my $title=$ARGV[0];
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8 $title =~ s/insertion.refined.bp/sorted.bam/;
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9 my $frag=$ARGV[1];
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11 open (input, "<$ARGV[0]") or die "Can't open $ARGV[0] since $!\n";
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12 print "Chr\tStart\tEnd\tTransposonName\tTransposonDirection\tClass\tVariantSupport\tFrequency\tJunction1\tJunction1Support\tJunction2\tJunction2Support\t5\'_Support\t3\'_Support\n";
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13 while (my $line=<input>) {
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14 chomp($line);
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15 my @a=split(/\t/, $line);
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17 my @b=split(/\(/, $a[6]);
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18 my @c=split(/\(/, $a[7]);
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19 my $terminal="5\'";
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20 my $reverse=0;
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21 my $positive=$b[0];
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22 my $negative=$c[0];
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23 if ($b[0] > $c[0]) {
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24 $terminal="3\'";
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25 $reverse=1;
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26 my $swap=$b[0];
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27 $b[0]=$c[0];
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28 $c[0]=$swap;
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29 }
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30 my $lower=$b[0]-$frag;
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31 my $upper=$c[0]+$frag;
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32 system("samtools view -Xf 0x2 $title $a[0]\:$lower\-$upper > temp.sam");
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34 open in,"temp.sam";
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35 my %ps=();
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36 my %me=();
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37 my $ref_sup=0;
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38 my $soft_clip=0;
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39 while(<in>)
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40 {
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41 chomp;
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42 my @f=split/\t/,$_,12;
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43 ## read number 1 or 2
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44 my ($rnum)=$f[1]=~/(\d)$/;
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45
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46 ## XT:A:*
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47 my ($xt)=$f[11]=~/XT:A:(.)/;
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48
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49 ## Coordinate
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50 if ($f[1]=~/r/)
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51 {
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52 my (@cigar_m)=$f[5]=~/(\d+)M/g;
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53 my (@cigar_d)=$f[5]=~/(\d+)D/g;
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54 my (@cigar_s)=$f[5]=~/(\d+)S/g;
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55 my (@cigar_i)=$f[5]=~/(\d+)I/g;
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56 my $aln_ln=sum(@cigar_m,@cigar_d);
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57 $me{$f[0]}=$f[3]+$aln_ln-1;
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58 }
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59 else
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60 {
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61 $ps{$f[0]}=$f[3];
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62 }
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63
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64 # ${$pe{$f[0]}}[$rnum-1]=[$xt,$coor];
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65 }
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66 close in;
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67
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68
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69 foreach my $id (keys %ps)
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70 {
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71 if (defined $me{$id})
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72 {
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73 if (((($ps{$id}+5)<=$positive)&&($me{$id}>$negative)) || ((($me{$id}-5)>=$negative)&&($ps{$id}<$positive))) {
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74 # if (((($ps{$id}+5)<=$b[0])&&($me{$id}>$c[0])) || ((($me{$id}-5)>=$c[0])&&($ps{$id}<$b[0]))) {
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75 $ref_sup++;
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76 # print "$id\n";
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77 }
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78 }
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79 }
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80
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81 my $variant=$a[8]+$a[9]+$a[10]+$a[11];
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82 my $ratio=sprintf("%.4f", $variant/($variant+$ref_sup));
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83 if (($a[0] =~ /^\d{1,2}$/) || ($a[0] eq "X") || ($a[0] eq "Y")) {$a[0]="chr$a[0]";}
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84 if ($reverse == 0) {
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85 print "$a[0]\t$a[1]\t$a[2]\t$a[3]\t$a[4]\t$a[5]\t$variant\t$ratio\t$b[0]\t$a[8]\t$c[0]\t$a[9]\t$a[10]\t$a[11]\n";
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86 }
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87 elsif ($reverse == 1) {
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88 print "$a[0]\t$a[1]\t$a[2]\t$a[3]\t$a[4]\t$a[5]\t$variant\t$ratio\t$b[0]\t$a[9]\t$c[0]\t$a[8]\t$a[10]\t$a[11]\n";
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89 }
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90 system("rm temp.sam");
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91 }
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92