annotate scripts/refine_breakpoint.ex.pl @ 0:28d1a6f8143f draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
author portiahollyoak
date Mon, 25 Apr 2016 13:08:56 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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2
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3 use strict;
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4
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5 my @files=<*.excision.cluster.*>;
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6 foreach my $file (@files) {
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7 if (($file !~ /sfcp/)&&($file !~ /refsup/)) {
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8 my $sfcp=$file.".sfcp";
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9 my $title=$file.".refined.bp";
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10
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11 open (input, "<$file") or die "Can't open $file since $!\n";
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12 open (input1, "<$sfcp") or die "Can't open $sfcp since $!\n";
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13 open (output, ">>$title") or die "Can't open $title since $!\n";
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14 print output "Chr\tStart\tEnd\tTransposonName\t5\'_Junction\t3\'_Junction\n";
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15 while (my $line=<input>) {
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16 chomp($line);
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17 my @a=split(/\s+/, $line);
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18 my $line1=<input1>;
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19 chomp($line1);
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20 my @b=split(/\t/, $line1);
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21 my @pos=split(/\;/, $b[4]);
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22 my $plusnext=""; my $minusnext="";
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23 my $plusover=0; my $minusover=0;
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24 my $lpcoor=""; my $lmcoor=""; my $rpcoor=""; my $rmcoor="";
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25 my $lp=0; my $lm=0; my $rp=0; my $rm=0;
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26 my %plus=(); my %minus=();
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27 foreach my $site (@pos) {
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28 my @x=split(/\:/, $site);
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29 my @y=split(/\(/, $x[0]);
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30 chop($y[1]);
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31 if (($y[0] =~ /\-/)&&($y[1] eq "+")&&($x[1] >= $plusover)) {
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32 if ($plusover >= 2) {$plusnext="$lpcoor\-$rpcoor\:$plusover";}
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33 $plusover=$x[1];
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34 my @z=split(/\-/, $y[0]);
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35 $lpcoor=$z[0]; $lp=$x[1];
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36 $rpcoor=$z[1]; $rp=$x[1];
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37 }
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38 elsif (($y[0] =~ /\-/)&&($y[1] eq "-")&&($x[1] >= $minusover)) {
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39 if ($minusover >= 2) {$minusnext="$lmcoor\-$rmcoor\:$minusover";}
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40 $minusover=$x[1];
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41 my @z=split(/\-/, $y[0]);
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42 $lmcoor=$z[0]; $lm=$x[1];
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43 $rmcoor=$z[1]; $rm=$x[1];
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44 }
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45 elsif (($y[0] !~ /\-/)&&($y[1] eq "+")) {
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46 $plus{$y[0]}=$x[1];
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47 }
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48 elsif (($y[0] !~ /\-/)&&($y[1] eq "-")) {
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49 $minus{$y[0]}=$x[1];
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50 }
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51 }
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52
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53 if (($plusnext ne "")&&($minusover == 0)) {
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54 my @m=split(/\:/, $plusnext);
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55 if (($m[1] >= 2)&&($m[1] == $plusover)) {
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56 my $count1=$m[1]; my $count2=$plusover;
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57 foreach my $id (keys %plus) {
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58 if ($m[0] =~ /$id/) {$count1 += $plus{$id};}
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59 elsif ($rpcoor == $id) {$count2 += $plus{$id};}
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60 }
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61 if ($count1 > $count2) {
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62 my @n=split(/\-/, $m[0]);
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63 $lpcoor=$n[0]; $lp=$m[1];
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64 $rpcoor=$n[1]; $rp=$m[1];
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65 }
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66 }
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67 }
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68
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69 if (($minusnext ne "")&&($plusover == 0)) {
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70 my @m=split(/\:/, $minusnext);
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71 if (($m[1] >= 2)&&($m[1] == $minusover)) {
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72 my $count1=$m[1]; my $count2=$minusover;
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73 foreach my $id (keys %minus) {
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74 if ($m[0] =~ /$id/) {$count1 += $minus{$id};}
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75 elsif ($lmcoor == $id) {$count2 += $minus{$id};}
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76 }
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77 if ($count1 > $count2) {
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78 my @n=split(/\-/, $m[0]);
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79 $lmcoor=$n[0]; $lm=$m[1];
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80 $rmcoor=$n[1]; $rm=$m[1];
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81 }
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82 }
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83 }
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84
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85 if (($plusover >= 2)&&($minusover >= 2)&&(($lpcoor-$rpcoor) != ($lmcoor-$rmcoor))) {
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86 if ($plusnext ne "") {
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87 my @m=split(/\:/, $plusnext);
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88 my @n=split(/\-/, $m[0]);
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89 if ((($n[1]-$n[0]) == ($rmcoor-$lmcoor))&&($m[1] >= 2)) {
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90 $rpcoor=$n[1];
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91 $lpcoor=$n[0];
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92 $plusover=$m[1];
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93 $lp=$m[1];
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94 $rp=$m[1];
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95 }
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96 }
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97 if ($minusnext ne "") {
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98 my @m=split(/\:/, $minusnext);
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99 my @n=split(/\-/, $m[0]);
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100 if ((($n[1]-$n[0]) == ($rpcoor-$lpcoor))&&($m[1] >= 2)) {
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101 $rmcoor=$n[1];
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102 $lmcoor=$n[0];
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103 $minusover=$m[1];
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104 $lm=$m[1];
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105 $rm=$m[1];
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106 }
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107 }
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108 }
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109
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110 my $plusc=0; my $pluscoor="";
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111 my $minusc=0; my $minuscoor="";
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112 foreach my $id (keys %plus) {
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113 if ($id eq $rpcoor) {
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114 $rp=$plusover+$plus{$id};
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115 }
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116 if ($plus{$id} > $plusc) {
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117 $plusc=$plus{$id};
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118 $pluscoor=$id;
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119 }
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120 elsif (($plus{$id} == $plusc)&&(abs($id-$b[2]) < abs($pluscoor-$b[2]))) {
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121 $plusc=$plus{$id};
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122 $pluscoor=$id;
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123 }
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124 }
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125 foreach my $id (keys %minus) {
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126 if ($id eq $lmcoor) {
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127 $lm=$minusover+$minus{$id};
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128 }
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129 if ($minus{$id} > $minusc) {
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130 $minusc=$minus{$id};
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131 $minuscoor=$id;
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132 }
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133 elsif (($minus{$id} == $minusc)&&(abs($id-$b[1]) < abs($minuscoor-$b[1]))) {
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134 $minusc=$minus{$id};
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135 $minuscoor=$id;
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136 }
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137 }
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138 if ($plusover < 2) {
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139 $lpcoor="";
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140 if ($plusc >= 3) {$rpcoor=$pluscoor; $rp=$plusc;}
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141 else {$rpcoor="";}
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142 }
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143 if ($minusover < 2) {
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144 $rmcoor="";
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145 if ($minusc >= 3) {$lmcoor=$minuscoor; $lm=$minusc;}
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146 else {$lmcoor="";}
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147 }
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148
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149 my $bp1=""; my $bp2="";
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150 if (($lpcoor ne "")&&($lmcoor ne "")) {
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151 $bp1="$lpcoor\(\+\)\:$lp,$lmcoor\(\-\)\:$lm";
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152 }
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153 elsif ($lpcoor ne "") {$bp1="$lpcoor\(\+\)\:$lp";}
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154 elsif ($lmcoor ne "") {$bp1="$lmcoor\(\-\)\:$lm";}
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155 if (($rpcoor ne "")&&($rmcoor ne "")) {
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156 $bp2="$rpcoor\(\+\)\:$rp,$rmcoor\(\-\)\:$rm";
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157 }
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158 elsif ($rpcoor ne "") {$bp2="$rpcoor\(\+\)\:$rp";}
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159 elsif ($rmcoor ne "") {$bp2="$rmcoor\(\-\)\:$rm";}
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160
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161 print output "$a[2]\t$a[3]\t$a[4]\t$a[5]\t$bp1\t$bp2\n";
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162 }
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163
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164 close input;
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165 close input1;
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166 close output;
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167 }
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168 }