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1 #!/usr/bin/perl -w
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2 #Filename:
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3 #Author: Tian Dongmei
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4 #Email: chentt@big.ac.cn
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5 #Date: 2014-05-21
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6 #Modified:
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7 #Description: merged deg file and total information
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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@","mark:s@","f:s","o=s","n=s","h");
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15 if (!(defined $opts{o} ) || defined $opts{h}) { #necessary arguments
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16 &usage;
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17 }
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18
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19 my @filein=@{$opts{'i'}};
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20 my @mark=@{$opts{'mark'}};
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21 my $fileout=$opts{'o'};
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22 my $number=$opts{'n'};
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23
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24 my %hash;
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25 open IN,"<$filein[0]"; #input file
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26
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27 while (my $aline=<IN>) {
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28 chomp $aline;
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29 next if($aline=~/^\"/);
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30 my @temp=split/\t/,$aline;
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31 $hash{$temp[0]}=$temp[4]."\t".$temp[6]."\t".$temp[7]."\t".$temp[-1];
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32 }
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33 close IN;
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34
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35 for (my $i=1;$i<=$#filein;$i++) {
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36 open IN,"<$filein[$i]"; #input file
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37
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38 while (my $aline=<IN>) {
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39 chomp $aline;
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40 next if($aline=~/^\"/);
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41 my @temp=split/\t/,$aline;
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42 if (!(defined $hash{$temp[0]})) {
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43 print "Not find $temp[0]in sample one!\n";
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44 next;
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45 }
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46 $hash{$temp[0]} .="\t".$temp[4]."\t".$temp[6]."\t".$temp[7]."\t".$temp[-1];
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47 }
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48 close IN;
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49 }
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50
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51 open OUT,">$fileout"; #output file
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52 my $deg_title;
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53 foreach (@mark) {
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54 $deg_title.="log2(Fold_change)\tp_value\tq_value\t".$_."\t";
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55 }
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56 $deg_title=~s/\s+$//;
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57 my %function;
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58 my $title;
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59 open F,"<$opts{f}";
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60 while (my $aline=<F>) {
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61 chomp $aline;
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62 if($aline=~/^\#/){
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63 my $title=$aline;
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64 my @title=split/\t/,$aline;
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65 $title[2+$number].="\t".$deg_title;
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66 $title=join"\t",@title;
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67 print OUT "$title\n";
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68 next;
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69 }
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70 my @temp=split/\t/,$aline;
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71 $temp[2+$number].="\t".$hash{$temp[0]};
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72 my $temp=join"\t",@temp;
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73 print OUT "$temp\n";
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74
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75 }
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76 close F;
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77 close OUT;
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78
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79 sub usage{
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80 print <<"USAGE";
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81 Version $version
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82 Usage:
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83 $0 -i -o -mark -f
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84 options:
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85 -i input file # -i output_score.txt -i output_score.txt -i output_score.txt
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86 -mark sample name # -mark sam1_VS_sam2 -mark sam1_VS_sam3 -mark sam2_VS_sam3
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87 -f cluster file
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88 -n sample number
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89 -o output file
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90 -h help
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91 USAGE
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92 exit(1);
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93 }
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94
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