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9
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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: tiandm@big.ac.cn
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5 #Date: 2010-01
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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 use File::Basename;
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13
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14 my %opts;
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15 GetOptions(\%opts,"i=s","min=i","max=i","o=s","mark:s","h");
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16 if (!(defined $opts{i} and defined $opts{o} and defined $opts{min} and defined $opts{max}) || defined $opts{h}) { #necessary arguments
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17 &usage;
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18 }
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19
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20 my $mark=defined $opts{'mark'} ? $opts{'mark'} : "Sample";
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21 my @mark=split /,/,$mark;
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22
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23
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24 open OUT,">$opts{o}";
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25 open IN,"<$opts{i}";
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26 my %hash;my %reads;
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27 while (my $aline=<IN>) {
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28 chomp $aline;
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29 my $seq=<IN>;
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30 chomp $seq;
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31
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32 if($aline=~/:([\d|_]+)_x(\d+)$/){
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33 my @ss=split/_/,$1;
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34 for (my $i=0;$i<@ss;$i++) {
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35 $hash{length($seq)}[$i]++ if($ss[$i]>0);
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50
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36 $hash{length($seq)}[$i] +=0 if($ss[$i]==0);
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9
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37 $reads{length($seq)}[$i]+=$ss[$i];
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38 }
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39 }
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40 #else{$reads{length($seq)}+=1;}
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41 if (length ($seq)>=$opts{'min'} && length ($seq) <=$opts{'max'}) {
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42 print OUT "$aline\n$seq\n";
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43 }
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44 }
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45 close IN;
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46 close OUT;
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47
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48 my $dir=dirname($opts{'o'});
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49 chdir $dir;
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50 my $lengthfile=$dir."/reads_length_distribution.txt";
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51 open OUT, ">$lengthfile";
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52 open R,">$dir/length_distribution.R";
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53
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54 print OUT "Tags length\t@mark\n";
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55
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56 my $samNo=@mark;
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57 my $avalue="";
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58 my @length=sort{$a<=>$b} keys %hash;
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59 foreach (@length) {
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60 print OUT $_,"\t@{$hash{$_}}\n";
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61 my $vv=join ", ",@{$hash{$_}};
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62 $avalue .="$vv,";
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63 }
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64 $avalue =~s/,$//;
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65 my $lengths=join ",",@length;
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66 my $marks=join "\",\"",@mark;
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67
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68 print R "a<-c($avalue)
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69 b<-matrix(a,ncol=$samNo,byrow=T)
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70 cl<-colors()
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71 names=c($lengths)
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72 legends=c(\"$marks\")
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73 png(\"Tags_length.png\",width=800,height=600)
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74 barplot(t(b),beside=TRUE,col=cl[1:$samNo],main=\"Tags Length Distribution\",names.arg=names,ylim=c(0,max(a)),legend.text=legends,args.legend=\"topleft\")
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75 abline(h=0)
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76 dev.off()
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77
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78 ";
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79 $avalue="";
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80 print OUT "\nReads length\t@mark\n";
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81 foreach (@length) {
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82 print OUT $_,"\t@{$reads{$_}}\n";
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83 my $vv=join ", ", @{$reads{$_}};
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84 $avalue .= "$vv,";
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85 }
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86 $avalue =~s/,$//;
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87
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88 print R "a<-c($avalue)\n
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89 b<-matrix(a,ncol=$samNo,byrow=T)
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90
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91 png(\"Reads_length.png\",width=800,height=600)
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92 barplot(t(b),beside=TRUE,col=cl[1:$samNo],main=\"Reads Length Distribution\",names.arg=names,ylim=c(0,max(a)),legend.text=legends,args.legend=\"topleft\")
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93 abline(h=0)
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94 dev.off()
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95
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96 ";
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97 close OUT;
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98 close R;
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99
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46
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100 #system ("R CMD BATCH $dir/length_distribution.R");
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9
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101
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102 #system ("rm $dir/length_distribution.R");
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103 #system ("rm $dir/length_distribution.Rout");
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104 #system ("rm $dir/.RData");
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105 sub usage{
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106 print <<"USAGE";
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107 Version $version
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108 Usage:
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109 $0 -i -o -min -max -mark
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110 options:
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111
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112 -i input file
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113 -o output file
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114 -min reads min length.
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115 -max reads max length.
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116 -mark string #sample name eg: samA,samB,samC
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117 -h help
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118 USAGE
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119 exit(1);
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120 }
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121
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