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t/InSilico/testModRes.pl  view on Meta::CPAN

#!/usr/bin/env perl
use strict;

use Carp;

BEGIN{
  use File::Basename;
  push @INC, (dirname $0).'/../../lib';
}

END{
}

use InSilicoSpectro::InSilico::ModRes;
use InSilicoSpectro;

InSilicoSpectro::init();
my $test = shift;

if ($test == 1) {
  print "******* list of all modif *********\n";
  foreach (InSilicoSpectro::InSilico::ModRes::getList()) {
    $_->print();
    print "=> ".$_->get('sprotFT')."\n";
  }
}

if ($test == 2) {
  print "******* given a FT, return the modif name *********\n";
  foreach ('PHOSPHORYLATION', 'N-acetylalanine', 'Phosphoserine (by PKC)]', 'ACETYLATION', 'SULFATION') {
    my $m=InSilicoSpectro::InSilico::ModRes::getModifFromSprotFT($_);
    print "$_ => ".((defined $m)?($m->get('name')):'unknown')."\n";
  }
}
if ($test == 3) {
  foreach ('PHOS', 'ACET_nterm', 'Oxidation', 'BIOT') {
    my $mr=InSilicoSpectro::InSilico::ModRes::getFromDico($_) || die "no modif for name=[$_]";
    print "modif ".$mr->{name}."\n";
    foreach my $seq (qw/LADELAKLVDVLEDK LDSVIEFSIPDSLLIR FASFEAQGALANIAVDK ETSGNLEQLLLAVVK SLEEIYLFSLPIK QNLFQEAEEFLYR TENLLGSYFPK VVLAYEPVWAIGTGK SPAGLQVLNDYLADK LISWYDNEFGYSNR SICTTVLELLDK /) {
      my @pos=$mr->seq2pos($seq);
      print "$seq -> [@pos]\n";
    }
    print "\n";
  }
}