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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: 2011/11/7
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6 #Modified:
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7 #Description: sam2BED
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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","o=s","h");
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15 if (!(defined $opts{i} 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 $filein=$opts{'i'};
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20 my $fileout=$opts{'o'};
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21 my $mark=$opts{'mark'};
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22 my @sample=split/\#/,$mark;
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23 $mark=join"\t",@sample;
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24 open OUT,">$fileout"; #output file
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25 print OUT "#chr\tstrand\tstart\tend\t$mark\n";
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26
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27 open IN,"<$filein"; #input file
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28 my $Tags_num=0;
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29 my @read_num;
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30 #print OUT "#chr\tstart\tend\tnum\t<=20\t21\t22\t23\t24\t>=25\n";
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31 while (my $aline=<IN>) {
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32 chomp $aline;
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33 next if($aline=~/^\@/);
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34 my @tmp=split/\t/,$aline;
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35 my $strand=$tmp[1];
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36 my $start=$tmp[3]+1;
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37 my $length=length($tmp[4]);
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38 my $end=$start+$length-1;
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39 my $hit=$tmp[6]+1;
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40 #======express caculate weighted===================================
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41 my $exp;
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42 my @tempID=split/\:/,$tmp[0];
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43 my @exp=split/\_/,$tempID[1];
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44 pop @exp;
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45 for (my $j=0;$j<@exp ;$j++) {
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46 #my @tempID1=split/\=/,$tempID[$j];
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47 $exp[$j]=sprintf("%.2f",$exp[$j]/$hit);
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48 $read_num[$j]+=$exp[$j];
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49 #print OUT "\t$exp";
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50 }
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51 $exp=join "\t",@exp;
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52 print OUT $tmp[2],"\t",$strand,"\t",$start,"\t",$end,"\t",$exp,"\n";
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53 $Tags_num++;
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54
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55 }
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56 print "Total Tags numer: $Tags_num\n";
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57 my $read_number=join "\t",@read_num;
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58 print "Each sample numer: $read_number\n";
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59 close IN;
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60 close OUT;
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61 sub usage{
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62 print <<"USAGE";
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63 Version $version
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64 Usage:
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65 $0 -i -o
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66 options:
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67 -i input file
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68 -mark sampleA sampleB sampleC.....
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69 -o output file
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70 -h help
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71 USAGE
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72 exit(1);
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73 }
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74
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