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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=(s=>"genomic",numberofbins=>20);
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6
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7
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8 GetOptions(\%opt, "f=s","version","gtf=s","range=i","annotation=s", "numberofbins=i","min_length=i","max_length=i","s=s","o=s","ignorestrand","outputall","sd=s","ssub=s","sdel=s","asd=s","assub=s","asdel=s","out=s","options","bins1=i","bins2=i","id=s");
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9
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10 my $cmnd;
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11
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12 my $prefix = "bc_$opt{id}";
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13
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14 if (exists $opt{version}){
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15 $cmnd = "python /usr/local/bin/pyBinCollector.py --version";
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16 }
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17 else{
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18 $cmnd = "python /usr/local/bin/pyBinCollector.py -f $opt{f} --gtf $opt{gtf} --annotation $opt{annotation} -o $prefix";
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19
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20 if(exists $opt{outputall})
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21 {
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22 $cmnd .= " --outputall";
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23 }
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24
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25 if(exists $opt{options}){
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26
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27 $cmnd .= " --range=$opt{range} --numberofbins $opt{numberofbins} --min_length $opt{min_length} --max_length $opt{max_length} -s $opt{s}";
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28
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29 if(exists $opt{ignorestrand}){ $cmnd .= " --ignorestrand";}
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30 if(exists $opt{bins1}){ $cmnd .= " --binselect $opt{bins1} $opt{bins2}";}
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31 }
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32 }
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33
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34
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35 system $cmnd;
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36 if(exists $opt{outputall}){
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37
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38 system "mv sense_data_$prefix.txt $opt{sd}";
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39 system "mv sense_subs_$prefix.txt $opt{ssub}";
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40 system "mv sense_dels_$prefix.txt $opt{sdel}";
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41 system "mv anti_sense_data_$prefix.txt $opt{asd}";
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42 system "mv anti_sense_subs_$prefix.txt $opt{assub}";
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43 system "mv anti_sense_dels_$prefix.txt $opt{asdel}";
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44 }
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45 else{
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46 system "mv $prefix"."_cumulative_densities_$opt{annotation}"."_$opt{s}_"."$opt{numberofbins}_bins.pileup $opt{out}";
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47 }
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