Using ModPipe from your own programs¶
It is possible to use ModPipe from your own programs. This can be done
in two ways. The first is simply to call the ModPipe script (modpipe)
from your own scripts, providing them with the
necessary configuration files and command line options, and then parsing any
output. The second is to import the ModPipe Python or Perl libraries into
your own Python or Perl programs. This can be done simply by adding
lib/python
or lib/perl
to your Python or Perl search path,
respectively. For example, to read in a ModPipe models file and print the
ID and DOPE score of each model (using the modpipe.serialize
module),
you can use a Python script similar to the following
(adjust /modpipe/location/
to the directory you have ModPipe
installed in):
import sys
sys.path.append('/modpipe/location/lib/python')
import modpipe.serialize
fh = open('d18b74a08d8b83e15835daaf76471976FCGHGNVV.mod')
for model in modpipe.serialize.read_models_file(fh):
print "Model: %s; DOPE score %f" % (model.id, model.score.dope)
The equivalent Perl script looks like:
use lib '/modpipe/location/lib/perl';
use PLLib::Utils;
use MPLib::Serialize;
my $fh = OpenFile('d18b74a08d8b83e15835daaf76471976FCGHGNVV.mod');
my $models = ReadModelsFile($fh);
close($fh);
for my $model (@$models) {
printf "Model: %s; DOPE score %f\n", $model->id, $model->score->dope;
}