hoge.pl

hoge.pl

use 5.14.2;
use warnings;
use Data::Dumper;
use SWISS::Entry;
use SWISS::IDs;
use JSON;
use GraphViz;
use GO::Parser;

use lib qw{../lib};
use UniProt;
use PhosphoSite;

my $uniprot = new UniProt('/Users/coela/projects/PhosphoViz/data/uniprot.tch',
        '/Users/coela/projects/PhosphoViz/data/uniprot_ac.tch');
my $ps = new PhosphoSite("/Users/coela/projects/PhosphoViz/data/Kinase_Substrate_Dataset");

#create_nodeattr($ps,$uniprot);
#network2json7($ps,$ARGV[0]);
#network2graphviz($ps);
#network2siff($ps);
#create_nodeattr($ps,$uniprot);
sub create_json_cerebral {

sub create_json_cerebral {
        my $ps = shift;
        my $uniprot = shift;
        my $file = shift;

        open my $XGMML, '<', $file or die;
        while (<$XGMML>) {
                chomp;
                if (/\<node label\="(\S+)" id="\S+">/){
                        say;
                }

        }
}



sub create_nodeattr {
        my $ps = shift;
        my $uniprot = shift;
        say 'Subcellar localization';
        for my $kinase ($ps->kinase()){
                my $sub_local = get_subcelluar_localization($ps, $uniprot,$kinase);
                if ($sub_local =~ /[Cc]ell [Jj]unction/) {
                        $sub_local = "Cell Junction";
                }
                elsif ($sub_local =~ /[Mm]embrane/) {
                        $sub_local = 'Membrane';
                }
                elsif ($sub_local =~ /[Cc]ytoplasm/) {
                        $sub_local = 'Cytoplasm';
                }
                elsif ($sub_local =~ /[Nn]ucleus/) {
                        $sub_local = 'Nucleus';
                }
#       say $kinase, ' = ', $sub_local; 
                say $sub_local;
        }
}