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Revision 1.1 - (view) (download) (as text)
| 1 : | mkubal | 1.1 | my $jobdir = shift(@ARGV); |
| 2 : | my $genome = shift(@ARGV); | ||
| 3 : | my $date = localtime(); | ||
| 4 : | |||
| 5 : | if(! -d "$jobdir/rp/$genome/attributes"){ | ||
| 6 : | `mkdir $jobdir/rp/$genome/attributes`; | ||
| 7 : | } | ||
| 8 : | |||
| 9 : | if(-e "$jobdir/rp/$genome/attributes/phenotypes.txt"){ | ||
| 10 : | |||
| 11 : | my $stain; | ||
| 12 : | open(IN,"$jobdir/rp/$genome/attributes/phenotypes.txt"); | ||
| 13 : | while($_ = <IN>){ | ||
| 14 : | if($_ =~/Gram_Stain\tPositive/){$stain = "positive";} | ||
| 15 : | elsif($_ =~/Gram_Stain\tNegative/){$stain = "negative";} | ||
| 16 : | } | ||
| 17 : | close(IN); | ||
| 18 : | |||
| 19 : | my $score_threshold; | ||
| 20 : | if($stain =~/(Negative|Positive)/){ | ||
| 21 : | if($stain eq "Negative"){$score_threshold = 2;} | ||
| 22 : | else{$score_threshold = 2.5;} | ||
| 23 : | $results = "/vol/seed-attributes/computation_results/Psort/$genome/$genome.output"; | ||
| 24 : | open(IN,$results); | ||
| 25 : | my $peg; | ||
| 26 : | my $record = 0; | ||
| 27 : | open(OUT,">$jobdir/rp/$genome/attributes/psort.txt"); | ||
| 28 : | while ($_ = <IN>){ | ||
| 29 : | chomp($_); | ||
| 30 : | if($record){ | ||
| 31 : | if($_ =~/(\w+)\s+(\d+.\d+)/){print OUT "$peg\tPSORT::$1\t$2\n";} | ||
| 32 : | elsif($_ =~/Unknown/){print OUT "$peg\tPSORT::unknown\tunknown\n";} | ||
| 33 : | $record = 0; | ||
| 34 : | } | ||
| 35 : | else{ | ||
| 36 : | if($_ =~/(fig\|\d+.\d+.peg.\d+)/){$peg = $1;} | ||
| 37 : | if($_ =~/(CytoplasmicMembrane)\s+(\d+.\d+)/){if($2 > $score_threshold){print OUT "$peg\tPSORT_score::$1\t$2\n";}} | ||
| 38 : | if($_ =~/(Cytoplasmic)\s+(\d+.\d+)/){if($2 > $score_threshold){print OUT "$peg\tPSORT_score::$1\t$2\n";}} | ||
| 39 : | if($_ =~/(OuterMembrane)\s+(\d+.\d+)/){if($2 > $score_threshold){print OUT "$peg\tPSORT_score::$1\t$2\n";}} | ||
| 40 : | if($_ =~/(Periplasmic)\s+(\d+.\d+)/){if($2 > $score_threshold){print OUT "$peg\tPSORT_score::$1\t$2\n";}} | ||
| 41 : | if($_ =~/(Extracellular)\s+(\d+.\d+)/){if($2 > $score_threshold){print OUT "$peg\tPSORT_score::$1\t$2\n";}} | ||
| 42 : | if($_ =~/(Cellwall)\s+(\d+.\d+)/){if($2 > $score_threshold){print OUT "$peg\tPSORT_score::$1\t$2\n";}} | ||
| 43 : | } | ||
| 44 : | if($_ =~/Final Prediction/){$record = 1} | ||
| 45 : | } | ||
| 46 : | close(OUT); | ||
| 47 : | } | ||
| 48 : | } | ||
| 49 : | |||
| 50 : |
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