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revision 1.1, Fri May 2 16:57:36 2008 UTC revision 1.2, Mon May 5 14:10:52 2008 UTC
# Line 8  Line 8 
8    
9  if(-e "$jobdir/rp/$genome/attributes/phenotypes.txt"){  if(-e "$jobdir/rp/$genome/attributes/phenotypes.txt"){
10    
11    
12      my $stain;      my $stain;
13      open(IN,"$jobdir/rp/$genome/attributes/phenotypes.txt");      open(IN,"$jobdir/rp/$genome/attributes/phenotypes.txt");
14      while($_ = <IN>){      while($_ = <IN>){
15          if($_ =~/Gram_Stain\tPositive/){$stain = "positive";}          if($_ =~/Gram_Stain\tPositive/){$stain = "Positive";}
16          elsif($_ =~/Gram_Stain\tNegative/){$stain = "negative";}          elsif($_ =~/Gram_Stain\tNegative/){$stain = "Negative";}
17      }      }
18      close(IN);      close(IN);
19    
20        print "$stain\n";
21    
22      my $score_threshold;      my $score_threshold;
23      if($stain =~/(Negative|Positive)/){      if($stain =~/(Negative|Positive)/){
24          if($stain eq "Negative"){$score_threshold = 2;}          if($stain eq "Negative"){$score_threshold = 2;}

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