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'))
def test_fill_doublegap(self):
"""Should insert fragments into correct sites."""
# prepare model
t = Template(DOUBLEGAP, 'file', 'A')
m = RnaModel()
for r in t:
m.copy_residue(r)
# insert first fragment
struc = ModernaStructure('file', FRAGMENT1)
f1 = ModernaFragment53(struc, anchor5=m['20'], anchor3=m['24'], \
new_sequence=Sequence('AUA'), keep=keep_first_last)
m.insert_fragment(f1)
resids = [r.identifier for r in m]
expected_resids1 = [
'18', '19', '20', '21', '21A', '23', '24', '27', '28', '29', '30',
'31', '32', '33', '34', '35'
]
self.assertEqual(resids, expected_resids1)
# insert second fragment
struc = ModernaStructure('file', FRAGMENT2)
f2 = ModernaFragment53(struc, anchor5=m['23'], anchor3=m['28'], \
new_sequence=Sequence('AUUA'), keep=keep_first_last)
m.insert_fragment(f2)
resids = [r.identifier for r in m]
expected_resids2 = [
'18', '19', '20', '21', '21A', '23', '24', '24A', '24B', '27',
'28', '29', '30', '31', '32', '33', '34', '35'
]
self.assertEqual(resids, expected_resids2)
def setUp(self):
self.s = ModernaStructure('file', MINI_TEMPLATE)
self.t = Template(MINI_TEMPLATE, 'file')
self.m = RnaModel(None, None, 'A', 'file', MINI_TEMPLATE)
self.f = ModernaFragment53(self.s,
anchor5=self.m['1'],
anchor3=self.m['14'])
self.struc = PDBParser().get_structure('test_struc', MINI_TEMPLATE)
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
def test_create_model_with_gaps(self):
"""Should create the model automatically."""
a = read_alignment(ALIGN_1B23_1QF6)
t = Template(RNA_1B23, 'file', 'R')
m = RnaModel(t, a)
m.apply_alignment()
m.insert_all_fragments()
self.assertEqual(
m.get_sequence().seq_with_modifications.replace('_', ''),
'GCCGAUAUAGCUCAGDDGGDAGAGCAGCGCAUUCGUEAUGCGAAG7UCGUAGGTPCGACUCCUAUUAUCGGCACCA'
)
def test_model_with_hydro_template(self):
"""If the template contains hydrogens, modifications should be added."""
t = Template(RNA_HYDRO, 'file', 'B')
a = read_alignment("""> 3tra_A.pdb Z73314.1/2358-2429
UPA
> 1qru_B.pdb X55374.1/1-72
CAA
""")
m = RnaModel(t, a)
m.create_model()
self.assertEqual(m.get_sequence(), Sequence('UPA'))
def test_number_gap(self):
"""Builds model with numbering gap in the template."""
a = read_alignment("""> target
CCGACCUUCGGCCACCUGACAGUCCUGUGCGGGAAACCGCACAGGACUGUCAACCAGGUAAUAUAACCACCGGGAAACGGUGGUUAUAUUACCUGGUACGCCUUGACGUGGGGGAAACCCCACGUCAAGGCGUGGUGGCCGAAGGUCGG
> template
CCGACCUUCGGCCACCUGACAGUCCUGUGCGG----CCGCACAGGACUGUCAACCAGGUAAUAUAACCACCGG----CGGUGGUUAUAUUACCUGGUACGCCUUGACGUGGGG----CCCCACGUCAAGGCGUGGUGGCCGAAGGUCGG
""")
t = Template(JMB_TEMPLATE, 'file')
clean_structure(t)
m = RnaModel(t, a)
m.create_model()
self.assertEqual(m.get_sequence().seq_without_breaks, a.target_seq)
def test_model_with_alignment_adjustment(self):
"""Introduces small corrections on alignment."""
a = read_alignment("""> target
ACUGUGAYUA[UACCU#P-G
> template with small errors.
GCG7A----U.UAGCUCA_G
""")
t = Template(MINI_TEMPLATE, 'file')
match_template_with_alignment(t, a)
m = RnaModel(t, a)
m.create_model()
self.assertEqual(m.get_sequence(), Sequence("ACUGUGAYUA[UACCU#PG"))
def test_doublegap_model(self):
"""Should create a model filling two gaps"""
a = read_alignment('''> target
GGGAUAGUUCCAGABU#A
> template
GGGA-AG--CCAGABU#A
''')
t = Template(DOUBLEGAP, 'file', 'A')
m = RnaModel(t, a)
m.apply_alignment()
m.insert_all_fragments()
m.fix_backbone()
self.assertEqual(m.get_sequence(), Sequence('GGGAUAGUUCCAGABU#A'))
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_oppositegap_model(self):
"""Should create a model with close gaps in the other respective sequence"""
a = read_alignment('''> target
GGGAGAGCRUUAG-BU#A
> template
GGGAGAGCR--AGABU#A
''')
t = Template(OPPOSITEGAP, 'file', 'A')
m = RnaModel(t, a)
m.apply_alignment()
m.insert_all_fragments()
self.assertEqual(
m.get_sequence().seq_with_modifications.replace('_', ''),
'GGGAGAGCRUUAGBU#A')
def test_model_with_close_gaps(self):
t = Template('test_data/rna_structures/2du3_excerpt.ent', 'file', 'D')
a = read_alignment('''> 1qru_B.pdb X55374.1/1-72
GCA-UUCCG
> 2du3_D.pdb
CUUUA-CCC
''')
m = RnaModel()
copy_some_residues([t['944'], t['946'], t['947']], m)
lc = find_fragment(m, '946', '947', Sequence('U'))
insert_fragment(m, lc[0])
lc = find_fragment(m, '944', '946', Sequence(''))
insert_fragment(m, lc[0])
return #TODO: remove
# generate model
m = RnaModel(t, a)
m.create_model()
def add_missing_3p(self):
""" """
if self.alignment and len(self.recipe.add_fragment_3p) > 0:
anchor5 = [r for r in self][-1]
ap_list = self.recipe.add_fragment_3p[0]
seq = Sequence(''.join(
[ap.target_letter.short_abbrev for ap in ap_list]))
all_resis = [r for r in Template(SINGLE_STRAND, 'file', 'A')]
while len(all_resis) - 1 < len(ap_list):
all_resis = self._elongate_strand(all_resis)
frag_resis = all_resis[:len(ap_list) + 1]
struc = ModernaStructure('residues', frag_resis)
frag = ModernaFragment5(struc,
anchor5=anchor5,
new_sequence=seq,
keep=keep_first)
self.insert_fragment(frag)
def test_fill_gap_numbering(self):
"""Should insert fragment with correct numbering."""
t = Template(DOUBLEGAP, 'file', 'A')
m = RnaModel()
for r in t:
m.copy_residue(r)
struc = ModernaStructure('file', FRAGMENT1)
f1 = ModernaFragment53(struc,
anchor5=m['20'],
anchor3=m['24'],
new_sequence=Sequence('AUA'))
m.insert_fragment(f1)
resids = [r.identifier for r in m]
expected_resids1 = [
'18', '19', '20', '20A', '20B', '20C', '24', '27', '28', '29',
'30', '31', '32', '33', '34', '35'
]
self.assertEqual(resids, expected_resids1)
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 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 test_gap_optimization_example_2(self):
t = Template('test_data/gaps/mini_1h4s_T_gap2.pdb', 'file', 'T')
a = read_alignment('test_data/gaps/ali_gap2.fasta')
m = RnaModel(t, a)
m.create_model()
def test_insert_indel_quality_1(self):
"""Insert a fragment without strand break"""
t = Template('test_data/gaps/mini_1h4s_T_gap2.pdb', 'file', 'T')
a = read_alignment('test_data/gaps/ali_gap2.fasta')
m = RnaModel(t, a)
self.assertEqual(m.get_sequence().seq_with_modifications.find('_'), -1)
def setUp(self):
self.a = read_alignment(MINI_ALIGNMENT)
self.a2 = read_alignment(MINI_ALIGNMENT_WITH_UNK)
self.t = Template(MINI_TEMPLATE, seq=Sequence("GCGGAUUUALCUCAG"))
self.m = RnaModel()
