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comparison quantify.pl @ 0:07745c0958dd draft

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author big-tiandm
date Thu, 18 Sep 2014 21:40:25 -0400
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1 #!/usr/bin/perl -w
2 #Filename:
3 #Author: chentt
4 #Email:
5 #Date: 2012-4-6
6 #Modified:
7 #Description:
8 my $version=1.00;
9
10 use strict;
11 use Getopt::Long;
12
13 my %opts;
14 GetOptions(\%opts,"i=s","o=s","d=s","h");
15 if (!(defined $opts{i} and defined $opts{d} and defined $opts{o}) || defined $opts{h}) { #necessary arguments
16 &usage;
17 }
18
19 my $input=$opts{'i'};
20 my $output=$opts{'o'};
21 my $depth=$opts{'d'};
22
23 open (IN,"<$input")||die"$!";
24 open OUT,">$output";
25 #my @Total=qw(15797079 18042650 17455254 17295526 18791753 16719596 15150009 18451484 17402501 17729362 19347595 17518516 15699663 16589265 15442892 14012264 14190746 17280260 13213117 12390121 14874304 );
26 my @Total=split/\,/,$depth;
27 #print OUT "#clusterID\tmajor_length\tpercent\n";
28 while (my $aline=<IN>) {
29 chomp $aline;
30 if ($aline=~/^\"/){
31 my @title=split/\t/,$aline;
32 for (my $i=0;$i<@title ;$i++) {
33 $title[$i]=~s/^\"(\S+)\"$/$1/;
34 }
35 my $title=join "\t",@title;
36 print OUT "\#$title\n";
37 next;
38 }
39 my @temp=split/\t/,$aline;
40 print OUT "$temp[0]\t$temp[1]\t$temp[2]";
41 my @id=split/:/,$temp[0];
42 my @posi=split/-/,$id[1];
43 for (my $i=3;$i<@temp;$i++) {
44 my $rpkm=sprintf("%.2f",$temp[$i]/($posi[1]-$posi[0]+1)/$Total[$i-3]*1000000000);
45 print OUT "\t$rpkm";
46 }
47 print OUT "\n";
48 }
49 close IN;
50 close OUT;
51
52 sub usage{
53 print <<"USAGE";
54 Version $version
55 Usage:
56 $0 -i -o -h
57 options:
58 -i input cluster file
59 -o output file
60 -d depth
61 -h help
62 USAGE
63 exit(1);
64 }