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1 #!/usr/bin/perl -w
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2 use strict;
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3 use Getopt::Long;
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4
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5 my %opt;
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6
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7
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8 GetOptions(\%opt, "gtf=s","po=s","version","mo=s","count=i","chromfile=s","t=s","iCLIP","track","name=s","description=s","color=s","s=s","id=s");
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9
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10 my $cmnd;
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11 my $prefix = "gb_$opt{id}";
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12 $prefix =~ s/\s/_/g;
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13
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14
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15 if (exists $opt{version}){
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16 $cmnd = "python /usr/local/bin/pyGTF2bedGraph.py --version";
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17 }
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18 else{
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19 $cmnd = "python /usr/local/bin/pyGTF2bedGraph.py --gtf $opt{gtf} --chromfile $opt{chromfile} -t $opt{t} --count $opt{count} -o $prefix";
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20
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21 if(exists $opt{iCLIP}){
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22
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23 $cmnd .= " --iCLIP";
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24 }
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25
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26 if(exists $opt{track}){
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27 $cmnd .= " --track --name \"$opt{name}\" --description \"$opt{description}\"";
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28
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29 if(exists $opt{color}){$cmnd .= " --color $opt{color}";}
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30 if(exists $opt{s}){$cmnd .= " -s \"$opt{s}\"";}
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31 }
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32 }
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33
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34 system $cmnd;
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35
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36 system "mv $prefix"."_plus_strand.bedgraph $opt{po}";
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37 system "mv $prefix"."_minus_strand.bedgraph $opt{mo}";
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38
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