def test_selected_targets_format(mock_open):
targets = {'a': 'coffee',
'b': 'tea'}
alignments = {}
for chain_id in targets:
alignments[chain_id] = TargetTemplateAlignment('', '')
alignments[chain_id].target_id = targets[chain_id]
path = tempfile.mktemp()
class FakeTarFile:
def __enter__(self, *args, **kwargs):
return self
def __exit__(self, *args, **kwargs):
pass
def extractfile(self, *args, **kwargs):
return open(path, 'r')
mock_open.return_value = FakeTarFile()
try:
modeler._write_selected_targets(alignments, path)
parsed = model_storage.extract_selected_targets('no.tar.gz')
finally:
if os.path.isfile(path):
os.remove(path)
eq_(parsed, targets)
def test_alignment_ok_for_range():
r = SequenceRange(1, 22, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA")
a = TargetTemplateAlignment(
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"-----AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA--")
ok_(domain_aligner._alignment_ok_for_range(r, a))
r = SequenceRange(1, 22, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA")
a = TargetTemplateAlignment(
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"-------GGGG------------------------------------")
ok_(not domain_aligner._alignment_ok_for_range(r, a))
def _merge_alignments(self, alignment1, alignment2):
span1 = alignment1.get_relative_span()
span2 = alignment2.get_relative_span()
# make sure span1 is the N-sided:
if span2 < span1:
span1, span2 = swap(span1, span2)
alignment1, alignment2 = swap(alignment1, alignment2)
# Determine alignment positions of span1 and span2:
i1 = 0
naa = 0
while naa < span1.end:
if is_amino_acid_char(alignment1.template_alignment[i1]):
naa += 1
i1 += 1
i2 = 0
naa = 0
while naa < span2.start:
if is_amino_acid_char(alignment2.template_alignment[i2]):
naa += 1
i2 += 1
return TargetTemplateAlignment(alignment1.target_alignment[: i1] + alignment2.target_alignment[i2: ],
alignment1.template_alignment[: i1] + alignment2.template_alignment[i2: ])
def test_count_aligned_residues():
alignment = BlastAlignment('pdb|1crn|A', 'AVAVAVAVAV', '',
1, 10, 'AVAVAVAVAV',
1, 10, 'A-A-A-A-A-')
eq_(alignment.count_aligned_residues(), 5)
alignment = TargetTemplateAlignment('AVAVAVAVAV',
'A-A-A-A-A-')
eq_(alignment.count_aligned_residues(), 5)
def test_get_percentage_identity():
alignment = BlastAlignment('pdb|1crn|A', 'AVAVAVAVAV', '',
1, 10, 'AVAVAVAVAV',
1, 10, 'ATATATATAT')
eq_(alignment.get_percentage_identity(), 50.0)
alignment = TargetTemplateAlignment('AVAVAVAVAV',
'ATATATATAT')
eq_(alignment.get_percentage_identity(), 50.0)
def test_get_percentage_coverage():
alignment = BlastAlignment('pdb|1crn|A', 'AVAVAVAVAV', '',
1, 10, 'AVAVAVAVAV',
1, 10, 'A-A-A-A-A-')
eq_(alignment.get_percentage_coverage(), 50.0)
alignment = TargetTemplateAlignment('AVAVAVAVAV',
'A-A-A-A-A-')
eq_(alignment.get_percentage_coverage(), 50.0)
def test_remove_enclosing():
d = {
SequenceRange(1, 22, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"):
TargetTemplateAlignment(
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV"),
SequenceRange(3, 18, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"):
TargetTemplateAlignment(
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV"),
SequenceRange(3, 20, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"):
TargetTemplateAlignment(
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV")
}
e = SequenceRange(2, 19, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA")
r = domain_aligner._remove_enclosing(e, d)
eq_(len(r), 2)
def align(self,
template_sequence,
template_secstr,
target_sequence,
gap_open=-13.0,
gap_extend=-0.4,
modifier=3.0):
_log.debug("kmad align\n{}\n{}\n{}".format(template_sequence,
template_secstr,
target_sequence))
# Prevent kmad from adding insertions in bulges, replace those.
template_secstr = self._remove_bulges(template_secstr, 'H', 3)
template_secstr = self._remove_bulges(template_secstr, 'E', 3)
if len(template_sequence) <= 0:
raise ValueError("empty template sequence")
if len(template_sequence) != len(template_secstr):
raise ValueError(
"template sequence ({}) has different length than secondary structure ({})"
.format(len(template_sequence), len(template_secstr)))
kmad_template_sequence = self._to_kmad_sequence(
template_sequence, template_secstr)
kmad_target_sequence = self._to_kmad_sequence(target_sequence)
input_path = tempfile.mktemp()
output_path = tempfile.mktemp()
write_fasta(input_path, {
'target': kmad_target_sequence,
'template': kmad_template_sequence
})
try:
self._run_kmad(input_path, output_path, gap_open, gap_extend,
modifier)
output_path += '_al'
aligned = parse_fasta(output_path)
_log.debug("kmad aligned\n{}\n{}".format(aligned['target'],
aligned['template']))
finally:
for path in [input_path, output_path]:
if os.path.isfile(path):
os.remove(path)
alignment = TargetTemplateAlignment(aligned['target'],
aligned['template'])
return alignment
def test_find_shared_hits_ranges():
d = {
SequenceRange(1, 22, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"):
TargetTemplateAlignment(
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV"),
SequenceRange(3, 18, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"):
TargetTemplateAlignment(
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV"),
SequenceRange(3, 19, "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"):
TargetTemplateAlignment(
"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
"VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV")
}
template_id = TemplateID('1xxx', 'A')
for v in d.values():
v.template_id = template_id
r = domain_aligner._find_shared_hits_ranges(d)
eq_(len(r), 1)
eq_(len(list(r.values())[0]), 3)
def test_get_template_sequence_in_target_range():
alignment = TargetTemplateAlignment(
"PHTSHSWLCDGRLLCLHDPSNKNNWKIFRECWKQGQPVLVSGVHKKLK" +
"SELWKPEAFSQEFGDQDVDLVNCRNCAIISDVKVRDFWDGFEIICKRL" +
"RSEDGQPMVLKLKDWPPGEDFRDMMPTRFEDLMENLPLPEYTKRDGRL" +
"NLASRLPSYFVRPDLGPKMYNAYGLITAEDRRVGTTNLHLDVSDAVNV" +
"MVYVGIPIGEG-AHDEEVLKTIDEGDADEVTKQRIHDGKEKPGALWHI" +
"YAAKDAEKIRELLRKVGEEQGQENPPDHDPIHDQSWYLDQTLRKRLYE" +
"EYGVQGWAIVQFLGDAVFIPAGAPHQVHNLYSCIKVAEDFVSPEHVKH" + "CFRLTQEF",
"-MIPHSWICEKHILWLKDYKNSSNWKLFKECWKQGQPAVVSGVHKKMN" +
"ISLWKAESISLDFGDHQADLLNCKD-SIISNANVKEFWDGFEEVSKR-" +
"-----ETVVLKLKDWPSGEDFKTMMPARYEDLLKSLPLPEYCNPEGKF" +
"NLASHLPGFFVR---GPRLCSAYGVVAAKDHDIGTTNLHIEVSDVVNI" +
"LVYVGIAKGNGILSKAGILKKFEEEDLDDILRKRLKDSSEIPGALWHI" +
"YAGKDVDKIREFLQKISKEQG------HDPIRDQSWYVNKKLRQRLLE" +
"EYGVRTCTLIQFLGDAIVLPAGALHQVQNFHSCIQVTEDFVSPEHLVE" + "SFHLTQEL")
range_ = SequenceRange(48, 96, alignment.target_alignment.replace('-', ''))
template_seq = domain_aligner._get_template_sequence_in_target_range(
alignment, range_)
eq_(template_seq, "ISLWKAESISLDFGDHQADLLNCKD-SIISNANVKEFWDGFEEVSKR-")
def test_get_relative_span():
alignment = TargetTemplateAlignment('---VA-AVAV-',
'--AAAAA-A-A')
r = alignment.get_relative_span()
eq_(r.start, 1)
eq_(r.end, 6)
def test_get_covered_template_residues_indices():
alignment = TargetTemplateAlignment('---VA-AVAV',
'A-AAAAA-A-')
indices = alignment.get_covered_template_residues_indices()
eq_(indices, [2, 3, 5, 6])
def _make_poly_A_alignment(self, context, chain_id):
template_seq = context.get_sequence(chain_id)
return TargetTemplateAlignment('A' * len(template_seq), template_seq)