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

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