annotate scripts/make.bp.bed.pl @ 10:3200a0299230 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit debe4684eaa00ffcae3c79e7581fdbe41da91d5d
author portiahollyoak
date Wed, 27 Apr 2016 11:44:13 -0400
parents 28d1a6f8143f
children 9672fe07a232
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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1 #! /usr/bin/perl
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2
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3 use strict;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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4
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5 my @sample=();
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6 open (in, "<$ARGV[0]") or die "Can't open $ARGV[0] since $!\n";
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7 my $line=<in>;
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8 close in;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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9
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10 my %chrs=();
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11 my @a=split(/\t/, $line);
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12 for my $i (0..$#a) {
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13 if ($a[$i] =~ /_class$/) {
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14 my $name=$a[$i];
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15 $name =~ s/_class//;
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16 my $j=$i+1;
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17 my $k=$i+2;
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18 my $l=$i+3;
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19 system("cut -f7,4,6,$j,$k,$l $ARGV[0] > temp");
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20 open (input, "<temp") or die "Can't open temp since $!\n";
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21 open (output, ">>$name.insertion.bp.bed") or die "Can't open $name.insertion.bp.bed since $!\n";
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22 my $header=<input>;
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23 while (my $line=<input>) {
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24 chomp($line);
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25 my @b=split(/\t/, $line);
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26 if (($b[4] ne "0")||($b[5] ne "0")) {
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27 my @c=split(/\:/, $b[2]);
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28 my @d=split(/\./, $c[1]);
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29 if ($d[0] > $d[1]) {
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30 my $temp=$d[0];
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31 $d[0]=$d[1];
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32 $d[1]=$temp;
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33 }
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34 my $lower=$d[0];
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35 my $upper=$d[1];
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36 if (($lower >= 0) && ($upper >= 0)) {
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37 print output "$c[0]\t$lower\t$upper\t$b[0]\t$b[1]\t$b[3]\t$b[4]\t$b[5]\n";
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38 }
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39 $chrs{$c[0]}=1;
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40 }
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41 }
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42 close input;
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43 close output;
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44 system("rm temp");
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45
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46 if ($ARGV[1] ne "") {
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47 open (input, "<$name.insertion.bp.bed") or die "Can't open $name.insertion.bp.bed since $!\n";
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48 open (output, ">tmp") or die "Can't tmp since $!\n";
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49 while (my $line=<input>) {
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50 chomp($line);
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51 my @a=split(/\t/, $line);
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52 if (($a[0] =~ /^\d{1,2}$/) || ($a[0] eq "X") || ($a[0] eq "Y")) {$a[0]="chr$a[0]";}
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53 my $strand="+";
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54 if ($a[4] eq "antisense") {$strand="-";}
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55 print output "$a[0]\t$a[1]\t$a[2]\t$a[3]\t\.\t$strand\t$a[5]\t$a[6]\t$a[7]\n";
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56 }
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57 close input;
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58 close output;
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59
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60 system("bedtools intersect -a tmp -b $ARGV[1] -f 0.1 -wo -s > tmp1");
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61 if ($ARGV[2] eq "") {
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62 system("awk -F \"\\t\" '{OFS=\"\\t\"; if ((\$4==\$13)&&(\$6==\$15)) print \$1,\$2,\$3,\$4,\$5,\$6}' tmp1 > tmp2");
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63 }
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64 else {
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65 my %family=();
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66 open (input, "<$ARGV[2]") or die "Can't open $ARGV[2] since $!\n";
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67 while (my $line=<input>) {
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68 chomp($line);
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69 my @a=split(/\t/, $line);
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70 $family{$a[0]}=$a[1];
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71 }
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72 close input;
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73
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74 open (input, "<tmp1") or die "Can't open tmp1 since $!\n";
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75 open (output, ">>tmp2") or die "Can't open tmp2 since $!\n";
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76 while (my $line=<input>) {
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77 chomp($line);
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78 my @a=split(/\t/, $line);
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79 if (($family{$a[3]} eq $family{$a[12]}) && ($a[5] eq $a[14])) {
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80 print output "$a[0]\t$a[1]\t$a[2]\t$a[3]\t$a[4]\t$a[5]\n";
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81 }
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82 }
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83 close input;
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84 close output;
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85 }
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86
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87 if (-s "tmp2") {
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88 system("bedtools subtract -a tmp -b tmp2 -f 1.0 > tmp3");
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89 open (input, "<tmp3") or die "Can't open tmp3 since $!\n";
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90 open (output, ">$name.insertion.bp.bed") or die "Can't open $name.insertion.bp.bed since $!\n";
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91 while (my $line=<input>) {
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92 chomp($line);
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93 my @a=split(/\t/, $line);
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94 my $direction="sense";
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95 if ($a[5] eq "-") {$direction="antisense";}
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96 my $chr_num=$a[0];
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97 $chr_num =~ s/chr//;
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98 if (($chrs{$a[0]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[0];}
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99 print output "$chr_num\t$a[1]\t$a[2]\t$a[3]\t$direction\t$a[6]\t$a[7]\t$a[8]\n";
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100 }
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101 close input;
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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102 close output;
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103 }
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104 }
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105
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106 system("rm tmp*");
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107
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108 }
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109 }
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110