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1 #!/usr/bin/perl -w
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2 #Filename:
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3 #Author: chentt
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4 #Email:
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5 #Date: 2012-4-6
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6 #Modified:
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7 #Description:
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8 my $version=1.00;
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9
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10 use strict;
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11 use Getopt::Long;
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12
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13 my %opts;
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14 GetOptions(\%opts,"i=s","o=s","d=s","h");
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15 if (!(defined $opts{i} and defined $opts{d} and defined $opts{o}) || defined $opts{h}) { #necessary arguments
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16 &usage;
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17 }
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18
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19 my $input=$opts{'i'};
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20 my $output=$opts{'o'};
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21 my $depth=$opts{'d'};
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22
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23 open (IN,"<$input")||die"$!";
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24 open OUT,">$output";
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25 #my @Total=qw(15797079 18042650 17455254 17295526 18791753 16719596 15150009 18451484 17402501 17729362 19347595 17518516 15699663 16589265 15442892 14012264 14190746 17280260 13213117 12390121 14874304 );
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26 my @Total=split/\,/,$depth;
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27 #print OUT "#clusterID\tmajor_length\tpercent\n";
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28 while (my $aline=<IN>) {
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29 chomp $aline;
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30 if ($aline=~/^\"/){
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31 my @title=split/\t/,$aline;
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32 for (my $i=0;$i<@title ;$i++) {
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33 $title[$i]=~s/^\"(\S+)\"$/$1/;
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34 }
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35 my $title=join "\t",@title;
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36 print OUT "\#$title\n";
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37 next;
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38 }
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39 my @temp=split/\t/,$aline;
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40 print OUT "$temp[0]\t$temp[1]\t$temp[2]";
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41 my @id=split/:/,$temp[0];
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42 my @posi=split/-/,$id[1];
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43 for (my $i=3;$i<@temp;$i++) {
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44 my $rpkm=sprintf("%.2f",$temp[$i]/($posi[1]-$posi[0]+1)/$Total[$i-3]*1000000000);
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45 print OUT "\t$rpkm";
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46 }
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47 print OUT "\n";
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48 }
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49 close IN;
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50 close OUT;
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51
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52 sub usage{
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53 print <<"USAGE";
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54 Version $version
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55 Usage:
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56 $0 -i -o -h
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57 options:
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58 -i input cluster file
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59 -o output file
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60 -d depth
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61 -h help
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62 USAGE
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63 exit(1);
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64 } |
