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1 #!/usr/bin/perl
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2
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3 # 27/04/2014
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4
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5 if($#ARGV==0){
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6 print "This program checks the number of baits in a Saint Output File.\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 $cutoff=0.01;
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13 while($i<=$#ARGV){
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14 if($ARGV[$i] eq '-i'){
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15 $i++;
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16 $ifile=$ARGV[$i];
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17 }
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18 else{
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19 die "\Incorrect program usage\n\n";
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20 }
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21 $i++;
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22 }
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23 }
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24
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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]+)/){
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33 if($1 ne $bait[$baitn]){
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34 $baitn++;
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35 $bait[$baitn]=$1;
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36 }
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37 }
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38 else{
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39 }
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40 }
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41 close(IFILE);
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42
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43 print $baitn;
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44
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45
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