def countKmersInitialized(seq, kLength, kmers):
k = len(seq)
# print seq
i = 0
while i + kLength <= k:
newWord = seq[i:i + kLength]
# print newWord
if kmers.has_key(newWord):
kmers[newWord] += 1
# print 'Found key forward'
elif kmers.has_key(aabpPyLib.reverseComplement(newWord, 'DNA')):
kmers[aabpPyLib.reverseComplement(newWord, 'DNA')] += 1
# print 'Found key reverse'
else:
# print 'Key should have been found, but was not'
pass
i += 1
return kmers
def countKmersFile(filename, kLength):
kmers = {}
fasta = {}
identifier = 0
fasta = inputFastaSeq(filename)
for entry in fasta:
k = len(fasta[entry])
i = 0
while i + kLength <= k:
newWord = fasta[entry][i:i + kLength]
if kmers.has_key(newWord):
kmers[newWord] += 1
elif kmers.has_key(aabpPyLib.reverseComplement(newWord, 'DNA')):
kmers[aabpPyLib.reverseComplement(newWord, 'DNA')] += 1
else:
kmers[newWord] = 1
i += 1
return kmers
def countKmersFile(filename, kLength):
kmers = {}
fasta = {}
identifier = 0
fasta = inputFastaSeq(filename)
for entry in fasta:
k = len(fasta[entry])
i = 0
while i + kLength <= k:
newWord = fasta[entry][i:i + kLength]
if kmers.has_key(newWord):
kmers[newWord] += 1
elif kmers.has_key(aabpPyLib.reverseComplement(newWord, 'DNA')):
kmers[aabpPyLib.reverseComplement(newWord, 'DNA')] += 1
else:
kmers[newWord] = 1
i += 1
return kmers
def countKmersInitialized(seq, kLength, kmers):
k = len(seq)
# print seq
i = 0
while i + kLength <= k:
newWord = seq[i:i + kLength]
# print newWord
if kmers.has_key(newWord):
kmers[newWord] += 1
# print 'Found key forward'
elif kmers.has_key(aabpPyLib.reverseComplement(newWord, 'DNA')):
kmers[aabpPyLib.reverseComplement(newWord, 'DNA')] += 1
# print 'Found key reverse'
else:
# print 'Key should have been found, but was not'
pass
i += 1
return kmers
def makeIsoform(kLength, seqLength, seqPortion, seqOriginal):
data = seqOriginal
alphabet = {0:'A', 1:'C', 2:'G', 3:'T'}
while data == seqOriginal:
data = seqPortion
while len(data) < seqLength:
if len(data) < seqLength:
data = data + alphabet[random.randint(0, len(alphabet)-1)]
else:
newNuc = alphabet[random.randint(0, len(alphabet)-1)]
if data[-1 * kLength -1: -1] + newNuc not in data and aabpPyLib.reverseComplement(data[-1 * kLength - 1: -1] + newNuc, 'DNA') not in data:
data = data + newNuc
return data
def makeSingleKmerPlusOneCountData(kLength, seqLength, repSeq, Ns):
data = repSeq
if Ns:
alphabet = {0:'A', 1:'C', 2:'G', 3:'T', 4:'N'}
else:
alphabet = {0:'A', 1:'C', 2:'G', 3:'T'}
while len(data) < seqLength:
if len(data) in range(0, kLength):
data = data + alphabet[random.randint(0, len(alphabet)-1)]
else:
newNuc = alphabet[random.randint(0, len(alphabet)-1)]
if data[-1 * kLength -1: -1] + newNuc not in data and aabpPyLib.reverseComplement(data[-1 * kLength - 1: -1] + newNuc, 'DNA') not in data:
data = data + newNuc
return data
def makeIsoform(kLength, seqLength, seqPortion, seqOriginal):
data = seqOriginal
alphabet = {0: 'A', 1: 'C', 2: 'G', 3: 'T'}
while data == seqOriginal:
data = seqPortion
while len(data) < seqLength:
if len(data) < seqLength:
data = data + alphabet[random.randint(0, len(alphabet) - 1)]
else:
newNuc = alphabet[random.randint(0, len(alphabet) - 1)]
if data[-1 * kLength - 1:
-1] + newNuc not in data and aabpPyLib.reverseComplement(
data[-1 * kLength - 1:-1] + newNuc,
'DNA') not in data:
data = data + newNuc
return data
def makeSingleKmerPlusOneCountData(kLength, seqLength, repSeq, Ns):
data = repSeq
if Ns:
alphabet = {0: 'A', 1: 'C', 2: 'G', 3: 'T', 4: 'N'}
else:
alphabet = {0: 'A', 1: 'C', 2: 'G', 3: 'T'}
while len(data) < seqLength:
if len(data) in range(0, kLength):
data = data + alphabet[random.randint(0, len(alphabet) - 1)]
else:
newNuc = alphabet[random.randint(0, len(alphabet) - 1)]
if data[-1 * kLength -
1:-1] + newNuc not in data and aabpPyLib.reverseComplement(
data[-1 * kLength - 1:-1] + newNuc, 'DNA') not in data:
data = data + newNuc
return data
