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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, "f=s","file_type=s","version","gtf=s","align_quality=i","align_score=i","range=i","length=i","max=i","distance=i","ignorestrand","overlap=i","unique","blocks","mutations=s","countoutput=s","stats=s","hittable=s","intronUTRoverlap=s","discarded=s","options","alignOpt","id=s");
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9
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10 my $cmnd;
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11 my $prefix = "rc_$opt{id}";
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12
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13
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14 if (exists $opt{version}){
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15 $cmnd = "python /usr/local/bin/pyReadCounters.py --version";
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16 }
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17 else{
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18 $cmnd = "python /usr/local/bin/pyReadCounters.py -f $opt{f} --file_type $opt{file_type} --gtf $opt{gtf} -o $prefix";
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19
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20 if(exists $opt{options}){
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21
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22 $cmnd .= " --range=$opt{range} --overlap=$opt{overlap}";
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23
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24 if(exists $opt{ignorestrand}){ $cmnd .= " --ignorestrand";}
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25 }
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26
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27 if(exists $opt{alignOpt}){
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28 $cmnd .= " --align_quality=$opt{align_quality} --align_score=$opt{align_score} --length=$opt{length} --distance=$opt{distance}";
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29 if(exists $opt{max}){$cmnd .= " --max=$opt{max}";}
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30 if(exists $opt{unique}){$cmnd .= " --unique";}
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31 if(exists $opt{blocks}){$cmnd .= " --blocks";}
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32 if(exists $opt{mutations}){$cmnd .= " --mutations=$opt{mutations}";}
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33 if(exists $opt{discarded}){$cmnd .= " --discarded=$opt{discarded}";}
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34
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35 }
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36 }
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37
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38
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39 system $cmnd;
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40 print STDOUT $cmnd;
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41
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42
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43 if(exists $opt{blocks}){
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44 system "mv $prefix"."_hittable_cDNAs.txt $opt{hittable}";
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45 system "mv $prefix"."_file_statistics_cDNAs.txt $opt{stats}";
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46 system "mv $prefix"."_intron_and_UTR_overlap_cDNAs.gtf $opt{intronUTRoverlap}";
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47
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48 if($opt{file_type} ne "gtf"){
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49 system "mv $prefix"."_count_output_cDNAs.gtf $opt{countoutput}";
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50 }
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51 }
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52 else{
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53 system "mv $prefix"."_hittable_reads.txt $opt{hittable}";
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54 system "mv $prefix"."_file_statistics_reads.txt $opt{stats}";
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55 system "mv $prefix"."_intron_and_UTR_overlap_reads.gtf $opt{intronUTRoverlap}";
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56
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57 if($opt{file_type} ne "gtf"){
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58 system "mv $prefix"."_count_output_reads.gtf $opt{countoutput}";
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59 }
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60 }
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