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1 require 'config.pl';
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2 open OUT, "> FISH/library_cis_list.txt";
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3 open OUT2, ">FISH/multi_test.txt";
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4
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5 $query1 = "select count(name) from cis_result_final_$proj where pvalueregion < $cocis_threshold and type = 'all_$library_percent' and gene_name not like '%BAD%' and region > 1 order by pvalueregion limit 100";
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6 $sth = $dbh->prepare("$query1");
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7
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8 $sth->execute;
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9
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10 while ((@row) = $sth->fetchrow_array) {
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11 $cis_number = $row[0];
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12 }
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13
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14 $query2="select name,gene_name, library_name from cis_result_final_$proj where pvalueregion < $cocis_threshold and type = 'all_$library_percent' and gene_name not like '%BAD%' and region > 1 order by pvalueregion limit 100";
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15
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16 $sth = $dbh->prepare("$query2");
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17 $sth->execute;
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18
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19 while ((@row) = $sth->fetchrow_array) {
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20 #print $row[2];
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21 @chunks = split(/::/m, $row[2]);
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22 foreach $lib(@chunks) {
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23 if ($lib ne '') {
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24 print OUT "$row[0]::$row[1]\t$lib\t1\n";
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25 }
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26 }
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27 }
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28 close OUT;
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29
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30 $sth = $dbh->prepare("select count(distinct descriptor) from metadata_$proj where descriptor != 'all';");
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31
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32 $sth->execute;
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33
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34 while ((@row) = $sth->fetchrow_array) {
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35 $desc_number = $row[0];
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36 }
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37 $ann_cis_testing = $desc_number*$cis_number;
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38 $cis_cis_testing = $cis_number*($cis_number-3)/2;
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39 $ann_ann_testing = $desc_number*($desc_number-3)/2;
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40 print OUT2 "$cis_number\t$desc_number\t$ann_cis_testing\t$cis_cis_testing\t$ann_ann_testing\n";
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41 close OUT2;
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42 $sth = $dbh->prepare("select 'descriptor', descriptor, library from metadata_$proj;");
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43 $sth->execute;
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44
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45 open OUT, "> FISH/library_descriptor_list.txt";
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46
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47 while ((@row) = $sth->fetchrow_array) {
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48 print OUT "$row[0]::$row[1]\t$row[2]\t1\n";
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49 }
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50
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51 close OUT;
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52
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53 open (my $list, ">", "FISH/list.txt");
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54 open (my $cis_list, "<", "FISH/library_cis_list.txt");
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55 while(<$cis_list>) {
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56 print $list $_;
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57 }
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58 close($cis_list);
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59 open (my $desc_list, "<", "FISH/library_descriptor_list.txt");
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60 while (<$desc_list>) {
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61 print $list $_;
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62 }
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63 close($desc_list);
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64 close($list);
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65 #system ("cat FISH/library_cis_list.txt FISH/library_descriptor_list.txt > FISH/list.txt");
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66 system ("perl lib/list2tab.pl 1 2 3 0 FISH/list.txt > FISH/cis4cluster.txt");
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67 system ("perl lib/list2tab.pl 1 2 3 0 FISH/library_cis_list.txt > results/Assoc/Cis.txt");
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68 system ("perl lib/list2tab.pl 1 2 3 0 FISH/library_descriptor_list.txt > results/Assoc/Ann.txt");
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69
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70 print "generated the matrix file cis4cluster.txt";
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71
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72
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