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Annotation of /FortyEight/rp_make_CELLO_attributes.pl

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1 : mkubal 1.1 my $jobdir = shift(@ARGV);
2 :     my $genome = shift(@ARGV);
3 :     my $date = localtime();
4 :    
5 :     opendir(DIR,$jobdir."/$genome");
6 : mkubal 1.2
7 :     if(! -d "$jobdir/rp/$genome/attributes"){
8 :     `mkdir $jobdir/rp/$genome/attributes`;
9 :     }
10 :    
11 :     open(CELLO,">$jobdir/rp/$genome/attributes/CELLO_attributes_for_$genome.txt");
12 : mkubal 1.1
13 :     print CELLO "$genome\tCELLO_computed_against_all_pegs\t$date\n";
14 :     @files = readdir(DIR);
15 :     foreach $file (@files){
16 :     if ($file =~/(\d+.\d+.peg.\d+).CELLO_result/){
17 :     $peg = $1;
18 :     open(IN,"$jobdir/$genome/$file");
19 :     my $score;
20 :     my $location;
21 :     while($_ = <IN>){
22 :     if($_ =~/(Membrane|Extracellular|CellWall|Cytoplasmic|Periplasmic|InnerMembrane|OuterMembrane)\s?..td..td..nbsp..nbsp..nbsp..nbsp.(\d.\d+).nbsp..nbsp.\*/){
23 :     $score = $2;
24 :     if($1 =~/^Membrane/){$location = "membrane"}
25 :     if($1 =~/Extracellular/){$location = "extracellular"}
26 :     if($1 =~/CellWall/){$location = "cell wall"}
27 :     if($1 =~/Cytoplasmic/){$location = "cytoplasm"}
28 :     if($1 =~/OuterMembrane/){$location = "outer membrane"}
29 :     if($1 =~/InnerMembrane/){$location = "inner membrane"}
30 :     if($1 =~/Periplasmic/){$location = "periplasm"}
31 :    
32 :     print CELLO "fig|$peg\tCELLO::$location\t$score\n";
33 :     }
34 :     }
35 :     close(IN);
36 :     }
37 :     }
38 :    
39 :     `rm $jobdir/$genome/*.CELLO_result`;

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