def gendnaword1to6(n, maptypetoparam):
"""
Generate and return a set of DNA words satisfying C1 and C6 constraints.
Inputs:
+ n: the number of strings to generate
+ maptypetoparam: a dictionary that maps an integer (representing the constraint type) to the parameter corresponding to that constraint type. It must have 1, 2, ..., 6 as keys
Output:
+ strlist: a Python list of DNA words satisfying C1 and C6 constraints
Example: to generate a set of 25 DNA words satisfying C1(8), C2(4), C3(5), C4(7), C5(8), C6(10), call the function
gendnaword1to6(25, {1 : 8, 2 : 4, 3 : 5, 4 : 7, 5 : 8, 6 : 10})
"""
if n <= 0:
return []
M = genbinword14(n, maptypetoparam[1], maptypetoparam[4])
# In M, change '0' to 'A' and '1' to 'T'
helper.change_char_in_mat(M, range(len(M[0])), {'0': 'A', '1': 'T'})
k = max(maptypetoparam[2], maptypetoparam[3], maptypetoparam[5],
maptypetoparam[6])
leadingstr = 'C' * k
# Append k = max(k2, k3, k5, k6) to the start of each row in M
strlist = []
for row in xrange(n):
strlist.append(leadingstr + ''.join(M[row]))
return strlist
def gendnaword1to6(n, maptypetoparam):
"""
Generate and return a set of DNA words satisfying C1 and C6 constraints.
Inputs:
+ n: the number of strings to generate
+ maptypetoparam: a dictionary that maps an integer (representing the constraint type) to the parameter corresponding to that constraint type. It must have 1, 2, ..., 6 as keys
Output:
+ strlist: a Python list of DNA words satisfying C1 and C6 constraints
Example: to generate a set of 25 DNA words satisfying C1(8), C2(4), C3(5), C4(7), C5(8), C6(10), call the function
gendnaword1to6(25, {1 : 8, 2 : 4, 3 : 5, 4 : 7, 5 : 8, 6 : 10})
"""
if n <= 0:
return []
M = genbinword14(n, maptypetoparam[1], maptypetoparam[4])
# In M, change '0' to 'A' and '1' to 'T'
helper.change_char_in_mat(M, range(len(M[0])), {'0': 'A', '1' : 'T'})
k = max(maptypetoparam[2], maptypetoparam[3], maptypetoparam[5], maptypetoparam[6])
leadingstr = 'C' * k
# Append k = max(k2, k3, k5, k6) to the start of each row in M
strlist = []
for row in xrange(n):
strlist.append(leadingstr + ''.join(M[row]))
return strlist
def gendnaword12378(n, maptypetoparam):
"""
Generate and return a set of DNA words satisfying C1, C2, C3, C7 and C8 constraints.
Inputs:
+ n: the number of strings to generate
+ maptypetoparam: a dictionary that maps an integer (representing the constraint type) to the parameter corresponding to that constraint type. It must have 1, 2, 3, 7 and 8 as keys.
Output:
+ strlist: a Python list of DNA words satisfying C1, C2, C3, C7 and C8 constraints
Example: to generate a set of 50 DNA words satisfying C1(8), C2(4), C3(5), C7(0.7), C8(3), call the function
gendnaword12378(50, {1 : 8, 2 : 4, 3 : 5, 7 : 0.7, 8 : 3})
"""
if n <= 0:
return []
if maptypetoparam[7] > 1:
return []
M = genbinword14(n, maptypetoparam[1], 1)
l0 = len(M[0])
if l0 & 1:
# If l0 is odd, append '0' at the end of every word in M so that
# the new length is even
for row in xrange(n):
M[row].append('0')
strlist = []
k = max(maptypetoparam[2], maptypetoparam[3])
for row in xrange(n):
newlist = ['1'] * k
newlist.extend(M[row])
newlist.extend(['1'] * k)
strlist.append(''.join(newlist))
# Break run
for strid in xrange(n):
strlist[strid] = algo_subroutine.breakrun(strlist[strid], maptypetoparam[8])
newlen = len(strlist[0])
chosencolumn = []
allcolumn = range(newlen)
if int(maptypetoparam[7]) == 1:
chosencolumn = range(newlen)
else:
chosencolumn = helper.choose_random_pos_list(newlen, int(math.ceil(maptypetoparam[7] * newlen)))
for strid in xrange(n):
curlist = list(strlist[strid])
helper.change_char_in_mat([curlist], chosencolumn, {'0': 'C', '1': 'G'})
helper.change_char_in_mat([curlist], allcolumn, {'0': 'A', '1':'T'})
strlist[strid] = ''.join(curlist)
return strlist
def gendnaword1to7(n, maptypetoparam):
"""
Generate and return a set of DNA words satisfying C1 and C7 constraints.
Inputs:
+ n: the number of strings to generate
+ maptypetoparam: a dictionary that maps an integer (representing the constraint type) to the parameter corresponding to that constraint type. It must have 1, 2, ..., 7 as keys.
Outputs:
+ strlist: a Python list of DNA words satisfying C1 and C7 constraints
Example: to generate a set of 25 DNA words satisfying C1(8), C2(4), C3(5), C4(7), C5(8), C6(10), C7(0.7), call the function
gendnaword1to7(25, {1 : 8, 2 : 4, 3 : 5, 4 : 7, 5 : 8, 6 : 10, 7 : 0.7})
"""
if n <= 0:
return []
if maptypetoparam[7] > 1:
return []
M = genbinword14(n, maptypetoparam[1], maptypetoparam[4])
k = max(maptypetoparam[2], maptypetoparam[3], maptypetoparam[5],
maptypetoparam[6])
l = len(M[0]) + k + k
chosencolumn = []
if int(maptypetoparam[7]) == 1:
chosencolumn = range(l)
else:
chosencolumn = helper.choose_random_pos_list(
l, int(math.ceil(maptypetoparam[7] * l)))
allcolumn = range(l)
strlist = []
for row in xrange(n):
# Append k instances of '1' at the beginning and the end of each row in M
newlist = ['1'] * k
newlist.extend(M[row])
newlist.extend(['1'] * k)
helper.change_char_in_mat([newlist], chosencolumn, {
'0': 'C',
'1': 'G'
})
helper.change_char_in_mat([newlist], allcolumn, {'0': 'A', '1': 'T'})
strlist.append(''.join(newlist))
return strlist
def gendnaword1to7(n, maptypetoparam):
"""
Generate and return a set of DNA words satisfying C1 and C7 constraints.
Inputs:
+ n: the number of strings to generate
+ maptypetoparam: a dictionary that maps an integer (representing the constraint type) to the parameter corresponding to that constraint type. It must have 1, 2, ..., 7 as keys.
Outputs:
+ strlist: a Python list of DNA words satisfying C1 and C7 constraints
Example: to generate a set of 25 DNA words satisfying C1(8), C2(4), C3(5), C4(7), C5(8), C6(10), C7(0.7), call the function
gendnaword1to7(25, {1 : 8, 2 : 4, 3 : 5, 4 : 7, 5 : 8, 6 : 10, 7 : 0.7})
"""
if n <= 0:
return []
if maptypetoparam[7] > 1:
return []
M = genbinword14(n, maptypetoparam[1], maptypetoparam[4])
k = max(maptypetoparam[2], maptypetoparam[3], maptypetoparam[5], maptypetoparam[6])
l = len(M[0]) + k + k
chosencolumn = []
if int(maptypetoparam[7]) == 1:
chosencolumn = range(l)
else:
chosencolumn = helper.choose_random_pos_list(l, int(math.ceil(maptypetoparam[7] * l)))
allcolumn = range(l)
strlist = []
for row in xrange(n):
# Append k instances of '1' at the beginning and the end of each row in M
newlist = ['1'] * k
newlist.extend(M[row])
newlist.extend(['1'] * k)
helper.change_char_in_mat([newlist], chosencolumn, {'0': 'C', '1': 'G'})
helper.change_char_in_mat([newlist], allcolumn, {'0': 'A', '1': 'T'})
strlist.append(''.join(newlist))
return strlist
def gendnaword14(n, maptypetoparam):
"""
Generate and return a set of DNA words satisfying C1 and C4 constraints.
Inputs:
+ n: the number of strings to generate
+ maptypetoparam: a dictionary that maps an integer (representing the constraint type) to the parameter corresponding to that constraint type. It must have 1 and 4 as keys
Output:
+ strlist: a Python list of DNA words satisfying C1 and C4 constraints
Example: to generate a set of 15 DNA words satisfying C1(8) and C4(9), call the function
gendnaword14(15, {1 : 8, 4 : 9 })
"""
if n <= 0:
return []
M = genbinword14(n, maptypetoparam[1], maptypetoparam[4])
helper.change_char_in_mat(M, range(len(M[0])), {'0': 'C', '1': 'G'})
return helper.convert_mat_to_strlist(M, n)
def gendnaword14(n, maptypetoparam):
"""
Generate and return a set of DNA words satisfying C1 and C4 constraints.
Inputs:
+ n: the number of strings to generate
+ maptypetoparam: a dictionary that maps an integer (representing the constraint type) to the parameter corresponding to that constraint type. It must have 1 and 4 as keys
Output:
+ strlist: a Python list of DNA words satisfying C1 and C4 constraints
Example: to generate a set of 15 DNA words satisfying C1(8) and C4(9), call the function
gendnaword14(15, {1 : 8, 4 : 9 })
"""
if n <= 0:
return []
M = genbinword14(n, maptypetoparam[1], maptypetoparam[4])
helper.change_char_in_mat(M, range(len(M[0])), {'0': 'C', '1': 'G'})
return helper.convert_mat_to_strlist(M, n)
def gendnaword1to8algo1(n, maptypetoparam):
"""
Generate and return a set of DNA words satisfying C1 through C8 constraints.
Inputs:
+ n: the number of strings to generate
+ maptypetoparam: a dictionary that maps an integer (representing the constraint type) to the parameter corresponding to that constraint type. It must have 1, 2, ..., 8 as keys.
Output:
+ strlist: a Python list of DNA words satisfying C1 through C8 constraints
Exception:
+ A RuntimeError will be raised if the following condition is NOT satified:
1 / (d + 1) <= gamma <= d / (d + 1)
where gamma = maptypetoparam[7] and d = maptypetoparam[8]
"""
gamma = maptypetoparam[7]
if n <= 0 or gamma > 1:
return []
d = maptypetoparam[8]
if (1.0 / (d + 1) > gamma) or (gamma > d * 1.0 / (d + 1)):
raise RuntimeError(
"gendnaword1to8algo1 works only if 1 / (d + 1) <= gamma <= d / (d + 1)"
)
# Generate the set of strings satisfies C1 constraint
M = genbinword14(n, max(maptypetoparam[1], maptypetoparam[4]), 1)
k = max([maptypetoparam[i] for i in xrange(2, 6 + 1)])
newM = []
for row in xrange(n):
newrow = []
newrow.extend(['1'] * k)
newrow.extend(M[row])
newrow.extend(['1'] * k)
newM.append(newrow)
# Find oddlist and evenlist as mentioned in Step 3 (see comments above)
newlen = len(newM[0])
newgamma = gamma
if newgamma < 0.5:
newgamma = 1 - newgamma
numchoose = int(newgamma * newlen)
numnotchoose = newlen - numchoose
minoddsize = int(numchoose * 1.0 / numnotchoose)
numleft = numchoose % numnotchoose
oddlist = []
evenlist = []
ind = 0
oddsize = 0
while ind < newlen:
oddlist.append(ind)
ind += 1
oddsize += 1
if ind < newlen and oddsize == minoddsize:
if numleft != 0:
oddlist.append(ind)
numleft -= 1
ind += 1
if ind < newlen:
evenlist.append(ind)
ind += 1
oddsize = 0
# Convert binary words into DNA words
if gamma < 0.5:
helper.change_char_in_mat(newM, oddlist, {'0': 'A', '1': 'T'})
helper.change_char_in_mat(newM, evenlist, {'0': 'C', '1': 'G'})
else:
helper.change_char_in_mat(newM, oddlist, {'0': 'C', '1': 'G'})
helper.change_char_in_mat(newM, evenlist, {'0': 'A', '1': 'T'})
return helper.convert_mat_to_strlist(newM, n)
def gendnaword1to8algo2(n, maptypetoparam):
"""
Generate and return a set of DNA words satisfying C1 through C8 constraints.
Inputs:
+ n: the number of strings to generate
+ maptypetoparam: a dictionary that maps an integer (representing the constraint type) to the parameter corresponding to that constraint type. It must have 1, 2, ..., 8 as keys.
Output:
+ strlist: a Python list of DNA words satisfying C1 through C8 constraints
Exception:
+ A RuntimeError will be raised if maptypetoparam[8] < 2
"""
if n <= 0:
return []
if maptypetoparam[7] > 1:
return []
if maptypetoparam[8] < 2:
raise RuntimeError(
"gendnaword1to8algo2 only works with maxlenrun >= 2")
# Generate the set of strings satisfies C1 constraint
M = genbinword14(n, max(maptypetoparam[1], maptypetoparam[4]), 1)
k = max([maptypetoparam[i] for i in xrange(2, 6 + 1)])
newM = []
l0 = len(M[0])
# Prepare the 'string' (list of characters) used later
baselist = ['1'] * (maptypetoparam[8] - 1)
baselist.append('0')
numtime = int(math.ceil(k * 1.0 / maptypetoparam[8]))
supplist = baselist * numtime
for row in xrange(n):
newrow = []
newrow.extend(supplist)
newrow.append('1')
sublen = 0
for ind in xrange(l0):
newrow.append(M[row][ind])
sublen += 1
if (sublen == maptypetoparam[8] - 1) or (ind == l0 - 1):
newrow.append(helper.get_complement_letter(M[row][ind]))
sublen = 0
newrow.append('0')
newrow.extend(supplist)
newM.append(newrow)
newlen = len(newM[0])
allcolumn = range(newlen)
if maptypetoparam[7] == 1:
chosencolumn = range(newlen)
else:
chosencolumn = helper.choose_random_pos_list(
newlen, int(math.ceil(maptypetoparam[7] * newlen)))
helper.change_char_in_mat(newM, chosencolumn, {'0': 'C', '1': 'G'})
helper.change_char_in_mat(newM, allcolumn, {'0': 'A', '1': 'T'})
return helper.convert_mat_to_strlist(newM, n)
def gendnaword12378(n, maptypetoparam):
"""
Generate and return a set of DNA words satisfying C1, C2, C3, C7 and C8 constraints.
Inputs:
+ n: the number of strings to generate
+ maptypetoparam: a dictionary that maps an integer (representing the constraint type) to the parameter corresponding to that constraint type. It must have 1, 2, 3, 7 and 8 as keys.
Output:
+ strlist: a Python list of DNA words satisfying C1, C2, C3, C7 and C8 constraints
Example: to generate a set of 50 DNA words satisfying C1(8), C2(4), C3(5), C7(0.7), C8(3), call the function
gendnaword12378(50, {1 : 8, 2 : 4, 3 : 5, 7 : 0.7, 8 : 3})
"""
if n <= 0:
return []
if maptypetoparam[7] > 1:
return []
M = genbinword14(n, maptypetoparam[1], 1)
l0 = len(M[0])
if l0 & 1:
# If l0 is odd, append '0' at the end of every word in M so that
# the new length is even
for row in xrange(n):
M[row].append('0')
strlist = []
k = max(maptypetoparam[2], maptypetoparam[3])
for row in xrange(n):
newlist = ['1'] * k
newlist.extend(M[row])
newlist.extend(['1'] * k)
strlist.append(''.join(newlist))
# Break run
for strid in xrange(n):
strlist[strid] = algo_subroutine.breakrun(strlist[strid],
maptypetoparam[8])
newlen = len(strlist[0])
chosencolumn = []
allcolumn = range(newlen)
if int(maptypetoparam[7]) == 1:
chosencolumn = range(newlen)
else:
chosencolumn = helper.choose_random_pos_list(
newlen, int(math.ceil(maptypetoparam[7] * newlen)))
for strid in xrange(n):
curlist = list(strlist[strid])
helper.change_char_in_mat([curlist], chosencolumn, {
'0': 'C',
'1': 'G'
})
helper.change_char_in_mat([curlist], allcolumn, {'0': 'A', '1': 'T'})
strlist[strid] = ''.join(curlist)
return strlist
def gendnaword1to8algo1(n, maptypetoparam):
"""
Generate and return a set of DNA words satisfying C1 through C8 constraints.
Inputs:
+ n: the number of strings to generate
+ maptypetoparam: a dictionary that maps an integer (representing the constraint type) to the parameter corresponding to that constraint type. It must have 1, 2, ..., 8 as keys.
Output:
+ strlist: a Python list of DNA words satisfying C1 through C8 constraints
Exception:
+ A RuntimeError will be raised if the following condition is NOT satified:
1 / (d + 1) <= gamma <= d / (d + 1)
where gamma = maptypetoparam[7] and d = maptypetoparam[8]
"""
gamma = maptypetoparam[7]
if n <= 0 or gamma > 1:
return []
d = maptypetoparam[8]
if (1.0 / (d + 1) > gamma) or (gamma > d * 1.0 / (d + 1)):
raise RuntimeError("gendnaword1to8algo1 works only if 1 / (d + 1) <= gamma <= d / (d + 1)")
# Generate the set of strings satisfies C1 constraint
M = genbinword14(n, max(maptypetoparam[1], maptypetoparam[4]), 1)
k = max([maptypetoparam[i] for i in xrange(2, 6 + 1)])
newM = []
for row in xrange(n):
newrow = []
newrow.extend(['1'] * k)
newrow.extend(M[row])
newrow.extend(['1'] * k)
newM.append(newrow)
# Find oddlist and evenlist as mentioned in Step 3 (see comments above)
newlen = len(newM[0])
newgamma = gamma
if newgamma < 0.5:
newgamma = 1 - newgamma
numchoose = int(newgamma * newlen)
numnotchoose = newlen - numchoose
minoddsize = int(numchoose * 1.0 / numnotchoose)
numleft = numchoose % numnotchoose
oddlist = []
evenlist = []
ind = 0
oddsize = 0
while ind < newlen:
oddlist.append(ind)
ind += 1
oddsize += 1
if ind < newlen and oddsize == minoddsize:
if numleft != 0:
oddlist.append(ind)
numleft -= 1
ind += 1
if ind < newlen:
evenlist.append(ind)
ind += 1
oddsize = 0
# Convert binary words into DNA words
if gamma < 0.5:
helper.change_char_in_mat(newM, oddlist, {'0': 'A', '1': 'T'})
helper.change_char_in_mat(newM, evenlist, {'0': 'C', '1': 'G'})
else:
helper.change_char_in_mat(newM, oddlist, {'0': 'C', '1': 'G'})
helper.change_char_in_mat(newM, evenlist, {'0': 'A', '1': 'T'})
return helper.convert_mat_to_strlist(newM, n)
def gendnaword1to8algo2(n, maptypetoparam):
"""
Generate and return a set of DNA words satisfying C1 through C8 constraints.
Inputs:
+ n: the number of strings to generate
+ maptypetoparam: a dictionary that maps an integer (representing the constraint type) to the parameter corresponding to that constraint type. It must have 1, 2, ..., 8 as keys.
Output:
+ strlist: a Python list of DNA words satisfying C1 through C8 constraints
Exception:
+ A RuntimeError will be raised if maptypetoparam[8] < 2
"""
if n <= 0:
return []
if maptypetoparam[7] > 1:
return []
if maptypetoparam[8] < 2:
raise RuntimeError("gendnaword1to8algo2 only works with maxlenrun >= 2")
# Generate the set of strings satisfies C1 constraint
M = genbinword14(n, max(maptypetoparam[1], maptypetoparam[4]), 1)
k = max([maptypetoparam[i] for i in xrange(2, 6 + 1)])
newM = []
l0 = len(M[0])
# Prepare the 'string' (list of characters) used later
baselist = ['1'] * (maptypetoparam[8] - 1)
baselist.append('0')
numtime = int(math.ceil(k * 1.0 / maptypetoparam[8]))
supplist = baselist * numtime
for row in xrange(n):
newrow = []
newrow.extend(supplist)
newrow.append('1')
sublen = 0
for ind in xrange(l0):
newrow.append(M[row][ind])
sublen += 1
if (sublen == maptypetoparam[8] - 1) or (ind == l0 - 1):
newrow.append(helper.get_complement_letter(M[row][ind]))
sublen = 0
newrow.append('0')
newrow.extend(supplist)
newM.append(newrow)
newlen = len(newM[0])
allcolumn = range(newlen)
if maptypetoparam[7] == 1:
chosencolumn = range(newlen)
else:
chosencolumn = helper.choose_random_pos_list(newlen, int(math.ceil(maptypetoparam[7] * newlen)))
helper.change_char_in_mat(newM, chosencolumn, {'0': 'C', '1': 'G'})
helper.change_char_in_mat(newM, allcolumn, {'0': 'A', '1': 'T'})
return helper.convert_mat_to_strlist(newM, n)