def processRead(path, contig_name=None):
print(path)
readSignal = np.array(getSignalFromRead(path), dtype=float)
readSignal = readSignal[fromRead:toRead]
readLevelString = getGlobalString(readSignal)
helperDict = {"a": "A", "b": "C", "c": "G", "d": "T"}
helperString = "".join(helperDict[i] for i in readLevelString)
levelHits = list(index.map(helperString))
if len(levelHits) == 0:
print("Return False.")
return False
for hit in levelHits:
diff = (hit.r_en - hit.r_st) - (hit.q_en - hit.q_st)
print("{0}: {1} vs {2}".format(hit.ctg, hit.r_en - hit.r_st,
hit.q_en - hit.q_st))
print("Position of hit is {0}".format(hit.r_st / lengths[hit.ctg]))
if diff < 0.05 * (hit.q_en - hit.q_st):
a, b = stringAllignment(str(refFasta[hit.ctg][hit.r_st:hit.r_en]),
helperString[hit.q_st:hit.q_en])
for i in range(1, 20):
print(i, ":", countDashes(a, i) + countDashes(b, i))
if contig_name != None and hit.ctg != contig_name:
print("Zle urceny contig!")
print("Return False.")
return False
print("Return True.")
return True
print("Return False.")
return False
from signalHelper import stringAllignment
assert stringAllignment("ACAATG", "ACAATG") == ("ACAATG", "ACAATG")
assert stringAllignment("ACXAATG", "ACAATG") == ("ACXAATG", "AC-AATG")
assert stringAllignment("TTT", "CCC") == ("---TTT", "CCC---")
from signalHelper import countDashes
assert countDashes("AAAC---AC--", 3) == 1
assert countDashes("AAAC---AC--", 2) == 1
assert countDashes("AAAC----A----", 4) == 2
refScale,
l,
overflow=0.30,
)
fakeStrings[l] = computeString(
fakeSignal,
0,
len(fakeSignal),
fakeShift,
fakeScale,
l,
overflow=0.30,
)
for l in levels:
a, b = stringAllignment(refStrings[l], readStrings[l])
c, d = stringAllignment(refStrings[l], fakeStrings[l])
# alignLenRead[levels.index(l)] += len(a)
# alignLenFake[levels.index(l)] += len(c)
alignLenRead[levels.index(l)] += len(readStrings[l])
alignLenFake[levels.index(l)] += len(fakeStrings[l])
# a = a[:300]
# b = b[:300]
# c = c[:300]
# d = d[:300]
dashes1 = [countDashes(a, i) + countDashes(b, i) for i in range(1, 21)]
dashes2 = [countDashes(c, i) + countDashes(d, i) for i in range(1, 21)]
fakeString = computeString(fakeSignal,
0,
len(fakeSignal),
fakeSignalShift,
fakeSignalScale,
levels,
overflow=0.30)
print("refstring vs Readstring vs fakestring")
print(refString)
print(readString)
print(fakeString)
print("Readstring allignment")
a, b = stringAllignment(refString, readString)
print(a)
print(b)
print("Fakestring allignment")
c, d = stringAllignment(refString, fakeString)
print(c)
print(d)
y = np.array(y, float)
refSignal = np.array(refSignal, float)
y -= ySignalShift
y /= ySignalScale
y[y < minSignal] = minSignal
fakeShiftSm,
fakeScaleSm,
levels,
overflow=0.25,
)
# print("readsm-1:",readString2Sm)
# print("refsm-1 :",refString2Sm)
# print("fakesm-1:",fakeString2Sm)
over1 = overlappingKmers(readString2Sm, refString2Sm, kmerLen)
over2 = overlappingKmers(fakeString2Sm, refString2Sm, kmerLen)
print("Overlap of len {0} -> good:{1} vs fake:{2}".format(
kmerLen, over1, over2))
a, b = stringAllignment(refString2Sm, readString2Sm)
c, d = stringAllignment(refString2Sm, fakeString2Sm)
oldGoodK = goodK
for i in range(0, len(a) - kmerLen + 1):
totalK += 1
goodK += 1
for j in range(i, i + kmerLen):
if a[j] == "-" or b[j] == "-":
goodK -= 1
break
if goodK != oldGoodK:
dobre += 1
print(f"Pocet {kmerLen}-ic je {goodK-oldGoodK}")
else:
hitLen = levelHits[0].r_en-levelHits[0].r_st
print("Hit len is {0}".format(hitLen))
print("Goodreads to all reads {0}/{1}".format(goodPosReads, counter))
'''
for i in levelHits:
print("Hit len is {0} from {1} to {2}".format(i.r_en-i.r_st, i.q_st, i.q_en))
print("Len of reference is {0}".format(len(contig)))
print("Len of refstring is {0}".format(len(refString)))
print("Hit je v {0}".format(hits[0].r_st/len(contig)))
print("Hit je v {0}".format(i.r_st/len(refString)))
counter += 1
'''
a, b = stringAllignment(refString[levelHits[0].r_st:levelHits[0].r_en], readString[levelHits[0].q_st:levelHits[0].q_en])
for i in range(1, 20):
print(i, ":", countDashes(a, i)+countDashes(b, i))
#x = overlappingKmers(refString[levelHits[0].r_st:levelHits[0].r_en],readString[levelHits[0].q_st:levelHits[0].q_en],kmerLen)
#print("Overlaps is {0}".format(x))
if counter >= posCounter:
break
print("\n\nNegative reads!\n")
print("*"*200)
for readFile in negReadsFiles[:negCounter]:
print(readFile)