def get_residue_num_list(cg, d):
'''
Get a list of nucleotides identifying a loop within
this element. If it's a stem, then pick a cycle
in the middle.
@param cg: A CoarseGrainRNA structure.
@param d: The name of the coarse-grain element
'''
return list(cg.define_residue_num_iterator(d, adjacent=True))
if d[0] == 'm':
return sorted(cg.shortest_bg_loop(d))
if (d[0] != 's'):
return list(cg.define_residue_num_iterator(d, adjacent=True))
stem_length = cg.stem_length(d)
start_res = cg.defines[d][0] + int(stem_length / 2)
pt = fus.dotbracket_to_pairtable(cg.to_dotbracket_string())
other_res = pt[start_res]
nucleotide_list = [start_res, start_res + 1, other_res - 1, other_res]
return nucleotide_list
def get_residue_num_list(cg, d):
'''
Get a list of nucleotides identifying a loop within
this element. If it's a stem, then pick a cycle
in the middle.
@param cg: A CoarseGrainRNA structure.
@param d: The name of the coarse-grain element
'''
return list(cg.define_residue_num_iterator(d, adjacent=True))
if d[0] == 'm':
return sorted(cg.shortest_bg_loop(d))
if (d[0] != 's'):
return list(cg.define_residue_num_iterator(d, adjacent=True))
stem_length = cg.stem_length(d)
start_res = cg.defines[d][0] + stem_length / 2
pt = fus.dotbracket_to_pairtable(cg.to_dotbracket_string())
other_res = pt[start_res]
nucleotide_list = [start_res, start_res+1,
other_res-1, other_res]
return nucleotide_list
def test_get_sides_plus(self):
db = ".((.).(.)).."
tuples = fus.pairtable_to_tuples(fus.dotbracket_to_pairtable(db))
c = _BulgeGraphConstruction(tuples)
p1 = c._get_sides_plus('s0', 'm0')
self.assertEquals(p1[0], 1)
p1 = c._get_sides_plus('s0', 'm2')
self.assertEquals(p1[0], 2)
p1 = c._get_sides_plus('s1', 'm0')
self.assertEquals(p1[0], 0)
def test_pairtable_to_elements(self):
db = "((((....))..))"
# 12345678901234
pt = fus.dotbracket_to_pairtable(db)
print("pt:", pt, file=sys.stderr)
elements = fus.pairtable_to_elements(pt, 0, 1, len(db))
self.assertTrue(['s', 2, [1, 2, 13, 14]] in elements)
self.assertTrue(['s', 4, [3, 4, 9, 10]] in elements)
self.assertTrue(['i', 3, [2, 3, 10, 11, 12, 13, ]])
self.assertTrue(['h', 5, [4, 5, 6, 7, 8, 9]])
print("pairtable_to_elements:", elements, file=sys.stderr)
def test_construction_ml(self):
db = "(.(.).(.).).."
tuples = fus.pairtable_to_tuples(fus.dotbracket_to_pairtable(db))
c = _BulgeGraphConstruction(tuples)
self.assertEqual(
c.defines, {
"s0": [1, 1, 11, 11],
"s1": [3, 3, 5, 5],
"s2": [7, 7, 9, 9],
"m0": [2, 2],
"m1": [6, 6],
"m2": [10, 10],
"h0": [4, 4],
"h1": [8, 8],
"t0": [12, 13]
})
self.assertEqual(c.edges["s1"], {"m0", "m1", "h0"})
def test_construction_rod(self):
db = "(((.(((...)))..)))"
tuples = fus.pairtable_to_tuples(fus.dotbracket_to_pairtable(db))
c = _BulgeGraphConstruction(tuples)
self.assertEqual(
c.defines, {
"s0": [1, 3, 16, 18],
"i0": [4, 4, 14, 15],
"s1": [5, 7, 11, 13],
"h0": [8, 10]
})
self.assertEqual(c.edges, {
"s0": {"i0"},
"i0": {"s0", "s1"},
"s1": {"i0", "h0"},
"h0": {"s1"}
})
def inverse_fold():
app.logger.info(request.json);
if not request.json:
abort(400, "Request has no json.")
if 'struct' not in request.json:
abort(400, "Request has no structure in the json.")
if re.match("^[\(\)\.]+$", request.json['struct']) is None:
abort(400, "Invalid structure for inverse fold: {}".format(request.json['struct']))
try:
pt = fus.dotbracket_to_pairtable(str(request.json['struct']))
except Exception as ex:
app.logger.exception(ex)
abort(400, "Unbalanced brackets: {}".format(ex))
result = RNA.inverse_fold("", str(request.json['struct']))[0]
return json.dumps(result), 201
def inverse_fold():
app.logger.info(request.json)
if not request.json:
abort(400, "Request has no json.")
if 'struct' not in request.json:
abort(400, "Request has no structure in the json.")
if re.match("^[\(\)\.]+$", request.json['struct']) is None:
abort(
400, "Invalid structure for inverse fold: {}".format(
request.json['struct']))
try:
pt = fus.dotbracket_to_pairtable(str(request.json['struct']))
except Exception as ex:
app.logger.exception(ex)
abort(400, "Unbalanced brackets: {}".format(ex))
result = RNA.inverse_fold("", str(request.json['struct']))[0]
return json.dumps(result), 201
def test_dotbracket_to_pairtable3(self):
db = "((((....))..)).((..)))"
with self.assertRaises(ValueError):
pt = fus.dotbracket_to_pairtable(db)
def test_dotbracket_to_pairtable1(self):
db = "....(((((.....((((((((((((.....(..(((....)))..)....))))))))))))......))))).."
fus.dotbracket_to_pairtable(db)
def test_dotbracket_to_pairtable(self):
"""
Convert a dotbracket string to a pair table.
"""
for pt, db in self.pt_dbs:
self.assertEqual(fus.dotbracket_to_pairtable(db), pt)
def test_pairtable_to_elements1(self):
db = "(.[.).]"
# 12345678901234
pt = fus.dotbracket_to_pairtable(db)
print("pt:", pt, file=sys.stderr)
def main():
usage = """
python scripts/dotplus.py sequence
Create a file for displaying as a dotplot using the provided sequence.
If the provided sequence is '-', then read the sequence from stdin.
"""
num_args = 1
parser = OptionParser(usage=usage)
parser.add_option(
'-p',
'--probability',
dest='probability',
default=0.01,
help="The probability cutoff for displaying base pair points",
type='float')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
if args[0] == '-':
seq = sys.stdin.read()
else:
seq = args[0].strip()
# pf_fold returns the MFE as well as the partition function energy
mfe, pfe = RNA.pf_fold(seq)
prob_matrix = RNA.export_bppm()
bp_to_seq = {}
# get all of the suboptimal structures
subopts = RNA.zukersubopt(seq)
for i in range(0, subopts.size()):
s = subopts.get(i)
pt = fus.dotbracket_to_pairtable(s.structure)
# go through each base pair and store the sequence
# it came from so that it can be output later
for j in range(1, pt[0] + 1):
bp = tuple(sorted([j, pt[j]]))
if bp in bp_to_seq:
continue
bp_to_seq[bp] = (s.structure, s.energy)
#print s.structure, s.energy
bps = []
structs = []
counter = 0
struct_dict = {}
base_probs = col.defaultdict(float)
print >> sys.stderr, "probability:", options.probability
for i, j in it.combinations(range(1, len(seq) + 1), 2):
prob = RNA.doubleP_getitem(prob_matrix,
RNA.intP_getitem(RNA.cvar.iindx, i) - j)
base_probs[i] += prob
base_probs[j] += prob
if prob > options.probability:
struct, energy = bp_to_seq[(i, j)]
pp = math.exp((pfe - (energy / 100.)) / .616310776)
if struct not in struct_dict:
struct_dict[struct] = (struct, pp, counter)
index = counter
counter += 1
else:
index = struct_dict[struct][2]
print >> sys.stderr, "ix:", index, "struct:", struct, "pp:", pp
bps += [{
"i": i,
"j": j,
"p": "{:.3f}".format(math.sqrt(prob)),
"ix": index
}]
structs = struct_dict.values()
structs.sort(key=lambda x: -x[1])
base_probs = dict([(i, "{:.3f}".format(j))
for (i, j) in base_probs.items()])
structs = [{
"struct": st[0],
"sprob": st[1],
"ix": st[2]
} for st in structs]
print json.dumps(
{
"seq": seq,
"structs": structs,
"bps": bps,
"baseProbs": base_probs.items()
},
indent=2)
def main():
usage = """
python scripts/dotplus.py sequence
Create a file for displaying as a dotplot using the provided sequence.
If the provided sequence is '-', then read the sequence from stdin.
"""
num_args= 1
parser = OptionParser(usage=usage)
parser.add_option('-p', '--probability', dest='probability', default=0.01, help="The probability cutoff for displaying base pair points", type='float')
#parser.add_option('-u', '--useless', dest='uselesss', default=False, action='store_true', help='Another useless option')
(options, args) = parser.parse_args()
if len(args) < num_args:
parser.print_help()
sys.exit(1)
if args[0] == '-':
seq = sys.stdin.read()
else:
seq = args[0].strip()
# pf_fold returns the MFE as well as the partition function energy
mfe, pfe = RNA.pf_fold(seq)
prob_matrix = RNA.export_bppm()
bp_to_seq = {}
# get all of the suboptimal structures
subopts = RNA.zukersubopt(seq)
for i in range(0, subopts.size()):
s = subopts.get(i)
pt = fus.dotbracket_to_pairtable(s.structure)
# go through each base pair and store the sequence
# it came from so that it can be output later
for j in range(1, pt[0]+1):
bp = tuple(sorted([j, pt[j]]))
if bp in bp_to_seq:
continue
bp_to_seq[bp] = (s.structure, s.energy)
#print s.structure, s.energy
bps = []
structs = []
counter = 0
struct_dict = {}
base_probs = col.defaultdict(float)
print >>sys.stderr, "probability:", options.probability
for i,j in it.combinations(range(1, len(seq)+1), 2):
prob = RNA.doubleP_getitem(prob_matrix,
RNA.intP_getitem(RNA.cvar.iindx, i) - j)
base_probs[i] += prob
base_probs[j] += prob
if prob > options.probability:
struct, energy = bp_to_seq[(i,j)]
pp = math.exp((pfe - (energy / 100.)) / .616310776)
if struct not in struct_dict:
struct_dict[struct] = (struct, pp, counter)
index = counter
counter += 1
else:
index = struct_dict[struct][2]
print >>sys.stderr, "ix:", index, "struct:", struct, "pp:", pp
bps += [{"i": i, "j": j, "p": "{:.3f}".format(math.sqrt(prob)), "ix": index}]
structs = struct_dict.values()
structs.sort(key=lambda x: -x[1])
base_probs = dict([(i, "{:.3f}".format(j)) for (i,j) in base_probs.items()])
structs = [{"struct": st[0], "sprob": st[1], "ix": st[2]} for st in structs]
print json.dumps({"seq": seq, "structs": structs, "bps": bps, "baseProbs": base_probs.items()}, indent=2)
def test_dotbracket_to_pairtable3(self):
db = "((((....))..)).((..)))"
pt = fus.dotbracket_to_pairtable(db)
