#!CHANGEJNET

use Env qw(JNET);

if ($JNET eq ""){
        print "Enrironment for JNET missing!\n";
        exit(0);
}
system ("rm -rf tmp.hmm tmp.prof");
system ("$JNET/bin/hmmbuild -F --fast --gapmax 1 --wblosum tmp.hmm $ARGV[0]");
system ("$JNET/bin/hmmconvert -F -p tmp.hmm tmp.prof");
system ("$JNET/perl/hmm2profile tmp.prof > $ARGV[0].hmmprof");
system ("rm tmp.hmm tmp.prof");
