def test_NW_score(hmat, decs, lecs):
"""Test for similarity in old and new alignment scoring
Complete NW version
"""
s1 = '6.2.1:2.3.1:1.2.4:2.7.1:4.2.1:5.4.2:2.7.2:1.2.1:4.1.2:2.7.1:5.3.1:5.4.2:3.1.3'
s1_ = '2.3.1:1.2.4:2.7.1:5.4.2:2.7.2:1.2.1'
# s2 = '1.2.4:2.3.1:2.3.3:4.1.1'
# s3 = '6.3.3:6.3.4:5.4.99:6.3.2:4.3.2:2.4.2:3.2.2'
ss1 = s1.split(':')
ss1_ = s1_.split(':')
# ss2 = s2.split(':')
# ss3 = s3.split(':')
ess = [ss1, ss1_]
for ii, i in enumerate(ess):
for ji, j in enumerate(ess):
score_old = nw.NW(hmat, lecs, ':'.join(i), ':'.join(j))[2]
score_new = nwx.NW(hmat, decs, i, j)[2]
assert abs(score_old - score_new) <= 1e-2
score_old_loc = nw.NW(hmat,
lecs,
':'.join(i),
':'.join(j),
local=True,
localize=True)[2]
score_new_loc = nwx.NW(hmat, decs, i, j, localize=True)[2]
assert abs(score_old_loc - score_new_loc) <= 1e-2
def align(ess_pair, nrdic):
"""Wraper for easy align ESS
Arguments:
- `ess_pair`: tuple. Pair of ess ids
"""
assert len(ess_pair) == 2, "Must be a pair of ess id"
id1, id2 = ess_pair
ess1 = nrdic[id1]
ess2 = nrdic[id2]
result = NW.NW(hmat, ecs, ess1, ess2, local=True)
score = result[2]
data = np.array([id1, id2, score], dtype=np.float32)
return data
def aliall_old(ind, seqs, mat, ecs):
"""Align the sequences in the specified index (ind) versus
all the rest of sequences
Keyword Arguments:
ind --
seqs --
"""
seq1 = seqs[ind]
result = []
print(ind)
for i in range(ind + 1, len(seqs)):
seq2 = seqs[i]
s1, s2, sco = nw.NW(mat, ecs, seq1, seq2)
result.append(sco)
return result
def align_ess_vs_real(rid, nrdic):
"""Wraper for easy align ESS
One random ESS versus all the real
Arguments:
- `rid`: nrdic, ress id (randome ess id)
"""
assert rid in nrdic, "ress must be in nrdic"
ress = nrdic[rid] # ress = random ess
scores = np.zeros(len(realdic), dtype=np.float32)
for nrid, v in realdic.iteritems():
ess = v['ec3']
result = NW.NW(hmat, ecs, ess, ress, local=True)
score = result[2]
scores[nrid - 1] = score
# fill mat
scomat[:, rid - 1] = scores
ss2 = s2.split(':')
ss3 = s3.split(':')
ess = [ss1, ss2, ss3, ss1_]
print("Test ESS:")
print('-' * 45)
print('1\t', nw.s1)
print('2\t', nw.s2)
print('3\t', nw.s3)
print('4\t', nw.s1_)
print('-' * 45, '\n')
print('\tSCORES')
print('-' * 45)
print('\t| Old\t| New')
print('s1-s2\t|Sco\tLoc\t|Sco\tLoc')
print('-' * 45)
line = '{}-{}\t|{:.3}\t{:.3}\t|{:.3}\t{:.3}'
for ii, i in enumerate(ess):
for ji, j in enumerate(ess):
sold = nw.NW(nw.hmat, lecs, ':'.join(i), ':'.join(j))[2]
snew = nwx.NW(nw.hmat, decs, i, j)[2]
soldl = nw.NW(nw.hmat,
lecs,
':'.join(i),
':'.join(j),
local=True,
localize=True)[2]
snewl = nwx.NW(nw.hmat, decs, i, j, localize=True)[2]
print(line.format(ii, ji, sold, soldl, snew, snewl))
decs = nw.decs
import pyximport
pyximport.install()
import dlist
import nw_ec_alignx as nwx
# subval = nw.__FastSubValues(nw.hmat, decs, nw.ss1, nw.ss2)
# align = dlist.FastNW(subval, nw.ss1, nw.ss2)
# arrow = align[1]
# arrowint = arrow.astype(np.int)
# back_ = dlist.backtrace(arrowint, nw.ss1, nw.ss2)
# back = nw.backtrace(arrow, nw.s1, nw.s2)
%timeit - n 100 nw.NW(nw.hmat, lecs, nw.s1, nw.s2)
%timeit - n 100 dlist.NW_(nw.hmat, decs, nw.ss1, nw.ss2)
%timeit - n 100 nwx.NW(nw.hmat, decs, nw.ss1, nw.ss2)
ess = [nw.ss1, nw.ss2, nw.ss3, nw.ss1_]
print('\tOld\t|\tNew')
print('Sco\tLoc\t|Sco\tLoc')
print('---------------------')
line = '{:.3}\t{:.3}\t|{:.3}\t{:.3}'
for i in ess:
for j in ess:
sold = nw.NW(nw.hmat, lecs, ':'.join(i), ':'.join(j))[2]
snew = nwx.NW(nw.hmat, decs, i, j)[2]
soldl = nw.NW(nw.hmat, lecs, ':'.join(i), ':'.join(j),
local=True, localize=True)[2]