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1 #!/usr/bin/perl -w
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2 #Filename:
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3 #Author: chentt
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4 #Email:
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5 #Date: 2012-4-6
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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
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13 my %opts;
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14 GetOptions(\%opts,"i=s","o=s","h");
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15 if (!(defined $opts{i} and defined $opts{o}) || defined $opts{h}) { #necessary arguments
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16 &usage;
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17 }
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18 open IN,"<$opts{i}";
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19 open OUT ,">$opts{o}";
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20 print OUT "#ID\tchr\tstart\tend\tstrand\n";
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21 my $n=1;
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22 my %gene1;
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23 while (my $aline=<IN>) {
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24 chomp $aline;
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25 next if($aline=~/^\#/);
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26 my @tmp=split/\t/,$aline;
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27 my $ID;
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28 if ($tmp[2] eq "gene") {
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29 $tmp[0]=~s/Chr\./Chr/;
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30 #$tmp[0]=~s/Chr/chr/;
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31 my @infor=split/;/,$tmp[8];
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32 for (my $i=0;$i<@infor ;$i++) {
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33 if ($infor[$i]=~/Alias\=(\S+)$/) {
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34 $ID=$1;
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35 last;
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36 }
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37 else {
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38 $ID="unknown$n";
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39 $n++;
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40 }
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41 }
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42 #$gene{$tmp[0]}{$ID}=[$tmp[3],$tmp[4],$tmp[6]];#$gene{chr}{geneID}=[start,end,strand]
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43 push @{$gene1{$ID}},[$tmp[3],$tmp[4],$tmp[0]];
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44 print OUT "$ID\t$tmp[0]\t$tmp[3]\t$tmp[4]\t$tmp[6]\n";
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45 }
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46 }
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47 close IN;
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48 close OUT;
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49
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50
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51 sub usage{
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52 print <<"USAGE";
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53 Version $version
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54 Usage:
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55 $0 -i -o -h
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56 options:
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57 -i input cluster file
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58 -o output file
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59 -h help
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60 USAGE
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61 exit(1);
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62 } |
