def test_build_model(self):
cmd = "python %smoderna.py -t %s -a %s -o %s > %s" % (
MODULE_PATH + os.sep, MINI_TEMPLATE, MINI_ALIGNMENT_FILE, self.tmp,
self.tmp2)
os.system(cmd)
t = Template(self.tmp)
self.assertEqual(t.get_sequence(), Sequence('ACUGUGAYUA[UACCU#PG'))
class RnaModelTests(TestCase):
def setUp(self):
self.a = read_alignment(MINI_ALIGNMENT)
self.t = Template(MINI_TEMPLATE, seq=Sequence("GCGGAUUUALCUCAG"))
self.m = RnaModel(self.t, self.a)
self.seq_before = self.t.get_sequence()
self.br = BaseRecognizer()
def tearDown(self):
self.a = None
self.t = None
self.m = None
self.br = None
self.seq_before = None
def test_insert_modi_chain(self):
cmd = "python %smoderna.py -s %s -c D -o %s -m m22G -p 38 > %s"%(MODULE_PATH+os.sep, RNA_HAIRPIN, self.tmp, self.tmp2)
os.system(cmd)
t = Template(self.tmp, template_chain_name='D')
self.assertEqual(t.get_sequence(),Sequence('CUGCCUQUC/RGC'))
def test_insert_modification(self):
cmd = "python %smoderna.py -s %s -o %s -m m22G -p 3 > %s"%(MODULE_PATH+os.sep, MINI_TEMPLATE, self.tmp, self.tmp2)
os.system(cmd)
t = Template(self.tmp)
self.assertEqual(t.get_sequence(),Sequence('GCRGAUUUALCUCAG'))
def load_template(file_path, chain_name='A'):
"""*load_template(file_path, chain_name='A')*
Loads a template structure from a PDB file.
Produces a Template object that can be saved in a variable.
Each template in ModeRNA has only one chain. By default, the chain
with id 'A' is loaded. Another chain id can be specified optionally
:Arguments:
* path+filename of a PDB structure file
* chain id (by default 'A')
"""
file_path = validate_filename(file_path)
t = Template(file_path, 'file', chain_name)
log.write_message('Template loaded from %s.\nTemplate sequence:\n%s\n' %(file_path, t.get_sequence().seq_with_modifications))
return t