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3
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1 #!/usr/bin/perl
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2
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3 # 17/12/2013
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4
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5 if($#ARGV==0){
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6 print "This program takes non-SaintExpress formatted data and converts it to look like it.\n";
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7 print "\nusage:\n $0\n-i [csv saint output file]\n\n";
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8 die;
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9 }
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10 else{
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11 $i=0;
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12 while($i<=$#ARGV){
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13 if($ARGV[$i] eq '-i'){
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14 $i++;
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15 $ifile=$ARGV[$i];
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16 }
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17 else{
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18 die "\Incorrect program usage\n\n";
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19 }
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20 $i++;
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21 }
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22 }
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23
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24 $i=0;
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25 $file='';
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26 open(IFILE,"<$ifile") || die "$ifile can't be opened: $!";
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27 { local $/=undef; $file=<IFILE>; }
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28 @lines=split /[\r\n]+/, $file;
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29 foreach $line (@lines) {
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30 if($line =~ /^Bait/){
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31 }
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32 elsif($line =~ /^([^\t]+)\t([^\t]+)\t([^\t]+)\t([^\t]+)/){
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33 $bait[$i]=$1;
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34 $prey[$i]=$2;
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35 $spec[$i]=$3;
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36 $fdr[$i]=$4;
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37 $i++;
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38 }
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39 else{
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40 }
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41 }
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42 close(IFILE);
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43 $line_count=$i;
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44
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45 open(OFILE, ">mockSaintExpress.txt");
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46 print OFILE "Bait\tPrey\tPreyGene\tSpec\tSpecSum\tAvgSpec\tNumReplicates\tctrlCounts\tAvgP\tMaxP\tTopoAvgP\tTopoMaxP\tSaintScore\tFoldChange\tBFDR\tboosted_by\n";
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47
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48 for($i=0; $i<$line_count; $i++){
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49 print OFILE "$bait[$i]\t111\t$prey[$i]\t111\t111\t$spec[$i]\t111\t111\t111\t111\t111\t111\t111\t111\t$fdr[$i]\t111\n";
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50 }
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51 close(OFILE);
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52
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