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1 #####################################################################################################################################################
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2 #Purpose: To perform blat and organize blat
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3 #Date: 07-19-2013
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4 #####################################################################################################################################################
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5 use Getopt::Long;
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6 #reading input arguments
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7 &Getopt::Long::GetOptions(
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8 'BLAT_PATH=s'=> \$blatpath,
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9 'REF_FILE=s'=> \$reffile,
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10 'INPUT_FILE=s' => \$inputfile,
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11 'OUTPUT_FILE=s' => \$outputfile,
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12 'MIN_SCORE=s'=> \$minScore,
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13 'MIN_IDENTITY=s'=> \$minidentity,
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14 'BLAT_PORT=s'=>\$blatport
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15 );
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16 $blatpath =~ s/\s|\t|\r|\n//g;
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17 $reffile=~ s/\s|\t|\r|\n//g;
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18 $inputfile=~ s/\s|\t|\r|\n//g;
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19 $outputfile=~ s/\s|\t|\r|\n//g;
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20 $minScore=~ s/\s|\t|\r|\n//g;
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21 $minidentity=~ s/\s|\t|\r|\n//g;
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22 $blatport=~ s/\s|\t|\r|\n//g;
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23 #input arguments
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24
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25 #checking for missing arguments
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26 if($blatport eq "" || $blatpath eq "" || $reffile eq "" || $inputfile eq "" || $outputfile eq "" || $minScore eq "" || $minidentity eq "")
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27 {
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28 die "missing arguments\n USAGE : perl perl_blat.pl -BLAT_PORT <BLAT_PORT> -MIN_SCORE <MIN_SCORE> -MIN_IDENTITY <MIN_IDENTITY> -BLAT_PATH <PATH TO BLAT FOLDER> -REF_FILE <PATH TO 2bit file> -INPUT_FILE <INPUT CONFIG FILE> -OUTPUT_FILE <OUTPUT FILE>\n";
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29 }
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30
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31 #parsing the arguments
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32
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33 #unless(-d $outdir)
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34 #{
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35 # system("mkdir -p $outdir");
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36 #}
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37 $status=`$blatpath/gfServer status localhost $blatport |wc -l`;
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38 chomp($status);
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39 $count = 0;
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40 while($status < 2 )
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41 {
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42 if($count > 0)
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43 {
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44 $blatport = $blatport+int(rand(1000))+1;
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45 }
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46 print "Starting the server\n";
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47 $sys ="$blatpath/gfServer start -canStop localhost $blatport $reffile &";
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48 print "$sys\n";
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49 system($sys);
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50 sleep(300);
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51 $status=`$blatpath/gfServer status localhost $blatport |wc -l`;
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52 chomp($status);
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53 $count++;
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54 if($count > 5)
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55 {
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56 die "something wrong with gfServer or command . Failed 5 times\n";
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57 }
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58 }
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59 print "querying \n";
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60 $sys = "$blatpath/gfClient localhost $blatport / $inputfile $outputfile -minScore=$minScore -minIdentity=$minidentity";
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61 print "$sys\n";
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62 system($sys);
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63 print "stoping the server\n";
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64 #$sys = "$blatpath/gfServer stop localhost $blatport";
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65 $pid = `ps|grep gfServer|head -1|cut -f1 -d ' '`;
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66 $sys ="kill -9 $pid";
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67 print "$sys\n";
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68 system($sys);
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