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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","version","gtf=s","range=i","overlap=i","--annotation=s", "--tab=s","--k_min=i","--k_max=i","--numberofkmers=i","--count=s","--features=s","--zscores=s","--random=s","options","o=s","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 $prefix = "m_$opt{id}";
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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/pyMotif.py --version";
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17 }
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18 else{
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19 $cmnd = "python /usr/local/bin/pyMotif.py -f $opt{f} --gtf $opt{gtf} --tab $opt{tab} --annotation $opt{annotation} -o $prefix";
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20
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21 if(exists $opt{options}){
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22
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23 $cmnd .= " --range=$opt{range} --overlap=$opt{overlap} --k_min=$opt{k_min} --k_max=$opt{k_max} --numberofkmers=$opt{numberofkmers}";
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24 }
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25 }
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26
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27 #testing
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28 #open (COUNT, ">$opt{count}") || die "";
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29 #print COUNT "$cmnd";
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30
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31 system $cmnd;
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32
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33
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34 system "mv $prefix"."_$opt{annotation}_data_k-mers_count.txt $opt{count}";
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35 system "mv $prefix"."_$opt{annotation}_top_k-mers_in_features.gtf $opt{features}";
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36 system "mv $prefix"."_$opt{annotation}_k-mer_Z_scores.txt $opt{zscores}";
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37 system "mv $prefix"."_$opt{annotation}_random_k-mers_count.txt $opt{random}";
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38
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39
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40
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41
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