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1 #!/usr/bin/perl -w
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2 use strict;
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3
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4 #creats a BED file with central area of peaks
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5
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6
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7 my $usage = qq{
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8 $0
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9
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10 -----------------------------
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11 mandatory parameters:
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12
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13 -f filename file with sites in BED format
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14 -l value length of the cental regions
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15
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16 -----------------------------
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17 optional parameters:
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18 -v for verbose
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19 -head 1/0 if there is a header
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20 -o filename output file
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21 };
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22
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23 if(scalar(@ARGV) <2){
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24 print $usage;
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25 exit(0);
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26 }
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27
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28 my $flank = 0;
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29 my $ResFilename = "";
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30 my $file = "";
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31 my $header = 0;
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32 my $verbose = 0;
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33
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34 while(scalar(@ARGV) > 0){
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35 my $this_arg = shift @ARGV;
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36 if ( $this_arg eq '-h') {print "$usage\n"; exit; }
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37 elsif ( $this_arg eq '-f') {$file = shift @ARGV;}
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38 elsif ( $this_arg eq '-v') {$verbose = 1;}
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39 elsif ( $this_arg eq '-head') {$header = shift @ARGV;}
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40 elsif ( $this_arg eq '-o') {$ResFilename = shift @ARGV;}
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41 elsif ( $this_arg eq '-l') {$flank = shift @ARGV;$flank /=2;}
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42 elsif ( $this_arg =~ m/^-/ ) { print "unknown flag: $this_arg\n";}
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43 }
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44
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45
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46
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47
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48 my $count = 0;
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49 my %hash;
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50
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51 open (FILE, "<$file") or die "Cannot open file $file!!!!: $!";
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52 open (OUT, ">$ResFilename") or die "Cannot open file $ResFilename!!!!: $!";
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53
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54 if ($header) {
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55 <FILE>;
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56 }
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57
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58 while (<FILE>) {
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59 s/\R//g;
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60 next if (/^#/);
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61 next if (/track/);
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62 next if (/summit/);
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63 my @a = split /\s/;
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64 my $chr = $a[0];
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65 my $maxPos = $a[3];
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66 my $score = $a[4];
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67 if ($maxPos=~/\D/) {
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68 $maxPos = int(($a[1]+$a[2])/2);
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69 } elsif ($maxPos < $a[1]){ #MACS intervals
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70 $maxPos = $a[1]+$a[4];
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71 $score = $a[5];
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72 }
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73 my $firstPos = $maxPos-$flank;
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74 my $lastPos = $maxPos+$flank;
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75
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76 my $ID=$chr.":".$firstPos."_".$lastPos."_".$score ;
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77 unless (exists($hash{$ID})) {
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78 $hash{$ID}=1;
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79 $count++;
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80 print OUT "$chr\t$firstPos\t$lastPos\t$score\n";
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81 }
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82 }
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83
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84 #print "$file\t$count\n";
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85 close FILE;
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86 close OUT;
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87
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