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1 : mkubal 1.1 #!/usr/bin/env /home/mkubal/public_html/FIGdisk/env/cee/bin/perl
2 :    
3 :     BEGIN {
4 :     @INC = qw(
5 :     /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib
6 :     /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/PPO
7 :     /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/FigKernelPackages
8 :     /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/WebApplication
9 :     /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/FortyEight
10 :     /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/SeedViewer
11 :     /home/mkubal/public_html/FIGdisk/dist/releases/dev/cee/lib/Flower
12 :     /home/mkubal/public_html/FIGdisk/dist/dev/cee/lib
13 :     /home/mkubal/public_html/FIGdisk/dist/dev/cee/lib/FigKernelPackages
14 :     /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/5.8.7/i686-linux
15 :     /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/5.8.7
16 :     /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/site_perl/5.8.7/i686-linux
17 :     /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/site_perl/5.8.7
18 :     /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/site_perl
19 :     /home/mkubal/public_html/FIGdisk/env/cee/lib/perl5/site_perl/5.8.7/Bio/Tools
20 :     .
21 :     /home/mkubal/public_html/FIGdisk/config
22 :    
23 :     );
24 :     }
25 :    
26 :     use Data::Dumper;
27 :     use Carp;
28 :     use FIG_Config;
29 :     $ENV{'BLASTMAT'} = "/home/mkubal/public_html/FIGdisk/BLASTMAT";
30 :     $ENV{'FIG_HOME'} = "/home/mkubal/public_html/FIGdisk";
31 :    
32 :     use SeqStats;
33 :     use pICalculator;
34 :     use FIG;
35 :    
36 :     open(MW,">/vol/seed-attributes/molecular_weight/molecular_weight.txt");
37 :     open(ISO,">/vol/seed-attributes/isoelectric_point/isoelectric_point.txt");
38 :    
39 :     $fig = new FIG;
40 :    
41 :     my @genomes = $fig->genomes('complete');
42 :     foreach my $genome (@genomes){
43 :     my @pegs = $fig->pegs_of($genome);
44 :     foreach $peg (@pegs){
45 :     my $seq = $fig->get_translation($peg);
46 :     $mw_seqobj = Bio::PrimarySeq->new(-seq=>$seq,
47 :     -alphabet=>'protein',
48 :     -id=>'test');
49 :    
50 :     $weight = Bio::Tools::SeqStats->get_mol_wt($mw_seqobj);
51 :     print MW "$peg\tmolecular_weight\t$$weight[0]\n";
52 :     #print "$peg\tmolecular_weight\t$$weight[0]\n";
53 :    
54 :     $pi_seqobj = Bio::Seq->new(-seq=>$seq,
55 :     -alphabet=>'protein',
56 :     -id=>'test');
57 :    
58 :     $calc = Bio::Tools::pICalculator->new(-places => 2);
59 :     $calc->seq($pi_seqobj);
60 :     $iep = $calc->iep;
61 :     print ISO "$peg\tisoelectric_point\t$iep\n";
62 :     #print "$peg\tisoelectric_point\t$iep\n";
63 :     }
64 :     }
65 :    

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