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2o_extension.py
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2o_extension.py
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#so far is making groups of nearest neighbor threes.
#search in the sequence itself for distance extenders.
#then fill that in with a selection of arms
#look more into the criteria for having a three arm.
#Should be able to cut many two threes after they don't lead to immediate extensions. Must be bounded by extension or lead directly into and extension.
#single arms don't need to be bounded by extension.
#Can start messing with this once make_arms has given 100% accurate list.
#search for long 2o extensions which include no mismatches and up to insert per side. enforce {00, 10, 01} extension order
#in the same way that hairpin size defines what can be a hairpin region and guides make_arms.py,
# long internal loopless matches guid the construction of the full 2o structure
#As the long internal matches are used by the RNA to choose correct arms form the search space, a long internal match overrules arms which overlap it
def listify(arms):
newarms=[]
for arm in arms:
newarm = eval(arm)
newarms.append(newarm)
return newarms
def piece_maker(s, size): #used to fragment sequence #Make 4 long min pieces? Use long pieces to look for matches first. Extend and try to build off 3bps and #Make file over in arm_maker and just read off of that.
pieces =[]
s = s# + s[0:biggest]
length = len(s)
j = 0 #beginning of piece
end = length-1 #end of piece
k=j+size
while j<length-size:
while k > j+size-2:
piece = s[j:k+1]
if piece.isalpha(): #for later when sequences with dashes are run through
pieces.append([piece, j, k+1]) # all the pieces with positional information #the positional tracking is off)
k = k - 1
#print k
j = j + 1
if j==length-size and j!=length:
size = size -1
k=j+size
#print pieces
return pieces
def piece_match2(pieces):
targets =[]
#print pieces
if pieces
for piece1 in pieces:
for piece2 in pieces:
if rna_hamming(piece1[0], piece2[0]) == 0:
if piece2[1]-piece1[2]>25:
target = piece1 + piece2
print target
print "extend out"
target = target_extend_outwards(target, s) #allowing 1 bp (non C) mismatch
#pair matching is off. Need to redo architecture to add on one base at a time,...
target = target_extend_inwards(target, s)
print target
targets.append(target)
return target
def rna_hamming(s1,s2): #sequence 1, sequence 2
#matches G's to T's/U's, A's to T's/U's, and G's to C's
#A hamming distance function that returns the hamming distance of the match between two ssRNA sequences.
#A hamming distance of 0 means a perfect match
s1rev = str(Seq(s1).reverse_complement())
the_zip = zip(s1rev, s2, s1[::-1])
hamming = 0
for charA, charB, charC in the_zip:
if charA == charB:
hamming = hamming + 0
elif charA == "C" and charB == "T" and charC == "G":
hamming = hamming + 0
elif charA == "A" and charB == "G" and charC == "T":
hamming = hamming + 0
elif charA == "C" and charB == "U" and charC == "G":
hamming = hamming + 0
elif charA == "A" and charB == "G" and charC == "U":
hamming = hamming + 0
elif charA == "-" or charB =="-" or charC == "-":
hamming = hamming + 0
else:
hamming = hamming + 1
return hamming
def target_extend_outwards(target, s): # used just for the initial seed
#add on outer end until hamming threshold is reached
if target[1] == 0:
return target
if target[5] ==len(s):
return target
targetA = target[0:3]
targetB = target[3:6]
leftbound = targetA[2]
rightbound = targetB[1]
count_gapA = 0
count_gapB = 0
hamm = 0
while hamm == 0:
tmptargetA = [s[targetA[1]-1:leftbound], targetA[1]-1, leftbound]
#print "TMP A" + str(tmptargetA)
tmptargetB = [s[rightbound:targetB[2]+1], rightbound, targetB[2]+1]
#print "TMP B" + str(tmptargetB)
hamm = rna_hamming(tmptargetA[0][0:1], tmptargetB[0][-1]) #just take hamming of the added on characters)
if hamm!= 0:
hamm = 0
tmptargetA = [s[targetA[1]-2:leftbound], targetA[1]-2, leftbound]
#print "TMP A" + str(tmptargetA)
tmptargetB = [s[rightbound:targetB[2]+1], rightbound, targetB[2]+1]
#print "TMP B" + str(tmptargetB)
hamm = rna_hamming(tmptargetA[0][0:1], tmptargetB[0][-1])
if hamm == 0:
count_gapA =1
targetA = tmptargetA
targetB = tmptargetB
else:
hamm = 0
tmptargetA = [s[targetA[1]-1:leftbound], targetA[1]-1, leftbound]
#print "TMP A" + str(tmptargetA)
tmptargetB = [s[rightbound:targetB[2]+2], rightbound, targetB[2]+2]
#print "TMP B" + str(tmptargetB)
hamm = rna_hamming(tmptargetA[0][0:1], tmptargetB[0][-1])
if hamm == 0:
targetA = tmptargetA
targetB = tmptargetB
else:
return (targetA + targetB)
else:
targetA=tmptargetA
targetB = tmptargetB
if targetA[1] == 0 or targetB[2] == len(s):
#print "end targetA {0}, and targetB {1}".format(targetA, targetB)
return (targetA + targetB)
#print "end targeta {0}, and targetB {1}".format(targetA, targetB)
return (targetA + targetB)
def target_extend_inwards(target, s):
#add on internally until hamming threshold is reached
if target[4]-target[2] < 28: # this is never happening
print "target already less than 28"
return target
targetA = target[0:3]
targetB = target[3:6]
leftbound = targetA[1]
rightbound = targetB[2]
hamm = 0
while hamm==0 and (targetB[1] - targetA[2]) > 28:
tmptargetA = [s[leftbound:targetA[2]+1], leftbound, targetA[2]+1]
tmptargetB = [s[targetB[1]-1:rightbound], targetB[1]-1, rightbound]
hamm = rna_hamming(tmptargetA[0], tmptargetB[0])
if hamm!=0# or (tmptargetB[1] - tmptargetA[2]) < 28:
hamm = 0
tmptargetA = [s[targetA[1]+2:leftbound], targetA[1]+2, leftbound]
#print "TMP A" + str(tmptargetA)
tmptargetB = [s[rightbound:targetB[2]-1], rightbound, targetB[2]-1]
#print "TMP B" + str(tmptargetB)
hamm = rna_hamming(tmptargetA[0][-1], tmptargetB[0][0:1])
if hamm == 0:
targetA = tmptargetA
targetB = tmptargetB
else:
hamm = 0
tmptargetA = [s[targetA[1]+1:leftbound], targetA[1]+1, leftbound]
#print "TMP A" + str(tmptargetA)
tmptargetB = [s[rightbound:targetB[2]-2], rightbound, targetB[2]-2]
#print "TMP B" + str(tmptargetB)
hamm = rna_hamming(tmptargetA[0][-1], tmptargetB[0][0:1])
if hamm == 0:
targetA = tmptargetA
targetB = tmptargetB
else:
return (targetA + targetB)
else:
targetA=tmptargetA
targetB = tmptargetB
#print "end targeta {0}, and targetB {1}".format(targetA, targetB)
return (targetA + targetB )
def seedmake(arms, s):
#Makes groups of 1, 2, and 3 to search for a geographic end
##
seeds = []
for arm1 in arms:
seeds.append(arm1)
prev = ''
count = 1
for arm2 in arms:
if (arm2[1]-arm1[5])>0 and (arm2[1]-arm1[5])< 8:
if count > 1 and arm2[1] == prev:
## print "2o extension2"
## print arm1
## print arm2
seed = [s[arm1[1]:arm2[5]], arm1[1], arm2[5]]
## print seed
seeds.append(seed)
## print '\n'
elif count == 1:
## print arm1
## print arm2
seed = [s[arm1[1]:arm2[5]], arm1[1], arm2[5]]
## print seed
seeds.append(seed)
prev = arm2[1]
count = count + 1
## print '\n'
count2 = 1
prev2 = ''
if len(arm1[0])>8:
for arm3 in arms:
if len(arm3[0]) >8:
if (arm3[1]-seed[2])>0 and (arm3[1]-seed[2])< 8:
#print "is this happening"
if count2 > 1 and arm3[1] == prev2:
## print "2o extension3"
## print seed
## print arm3
seed = [s[seed[1]:arm3[5]], seed[1], arm3[5]]
## print seed
seeds.append(seed)
## print '\n'
elif count2 == 1:
## print "2o extension3"
## print seed
## print arm3
seed = [s[seed[1]:arm3[5]], seed[1], arm3[5]]
#print seed
seeds.append(seed)
prev2 = arm3[1]
count2 = count2 + 1
## print '\n'
return seeds
def closerange_target_extend(target,s, order): #index tracking is off on both sides, but offsets are working.
#print "enter closerange"
#print "target: {0}".format(target)
if target[1] <= 4:
return target
if target[5] >=len(s)-2:
return target
#gap = target[6]
tmptargetA = target[0:3]
tmptargetB = target[3:6]
leftbound = tmptargetA[2]
rightbound = tmptargetB[1]
hamm = 0
count = 1
testcycles = 0
#extension_order = [[0, 1], [1, 0], [1, 1], [1, 2], [2, 1], [0,2], [2, 0],[2, 2]] #02, 20 come after 12, 21
if order == "long":
extension_order = ['00', '10', '01', '11', '02', '20', '22', '03', '30', '04', '40', '05', '50', '06', '60', '21', '12','31', '13', '23', '32', '33', '42', '24', '43', '34', '44', '52', '25', '53', '35', '54', '45', '55', '63', '36', '64', '46', '65', '56', '66', '74', '47', '75', '57', '76', '67', '77', '87', '78', '88', '89', '98', '99']
setthatneeds4 = ['03', '30']
setthatneeds5 = ['04', '40', '05', '50', '06', '60']
while testcycles <len(extension_order):
#print "testcycles: {0}".format(testcycles)
hamm = 0
extensionA= "placeholder"
extensionB= "placeholder"
extend = 1
extendAseed = int(extension_order[testcycles][:1])
extendBseed = int(extension_order[testcycles][-1])
count = 0
##print "enterhamming loop"
#print extension_order[testcycles]
while hamm == 0 and extensionA:
#current_gap = gap + max(extension_order[testcycles][0], extension_order[testcycles][1])
newtarget = [s[tmptargetA[1]-len(extensionA): leftbound], tmptargetA[1]-len(extensionA), leftbound, s[rightbound: tmptargetB[2]+ len(extensionB)], rightbound,tmptargetB[2]+len(extensionB)]
#print "running..." + str(count)
extensionA = s[tmptargetA[1]-extendAseed-extend:tmptargetA[1]]
extensionB = s[tmptargetB[2]:tmptargetB[2]+extendBseed+extend]
hamm = hamm + rna_hamming(extensionA[0:1], extensionB[-1])
#print "this went to hamm, extensionAbegin : {0}, extensionBend: {1}".format(extensionA[0:1], extensionB[-1])
#print "targetA, target B, extensionA, extentionB: {0}, {1}, {2}, {3}".format(tmptargetA, tmptargetB, extensionA, extensionB)
extend = extend + 1
count = count + 1
#print count
#print testcycles
if count<3:
testcycles = testcycles + 1
elif extension_order[testcycles] in setthatneeds4:
if count>4:
#print "found one in set that needs 4"
#print "about to be returned : {0}".format(newtarget)
dashedA = str(newtarget[0][0:count-1])+(extendAseed)*'-'+ str(target[6])
dashedB = str(target[7])+extendBseed*'-'+ str(newtarget[3][-(count-1):])
newtarget.append(dashedA)
newtarget.append(dashedB)
#print dashedA
#print dashedB
#print newtarget
#print '\n'
return newtarget
else:
testcycles = testcycles + 1
elif extension_order[testcycles] in setthatneeds5:
if count>5:
#print "found one in set that needs 5"
#print "about to be returned : {0}".format(newtarget)
dashedA = str(newtarget[0][0:count-1])+(extendAseed)*'-'+ str(target[6])
dashedB = str(target[7])+extendBseed*'-'+ str(newtarget[3][-(count-1):])
newtarget.append(dashedA)
newtarget.append(dashedB)
#print dashedA
#print dashedB
#print newtarget
#print '\n'
return newtarget
else:
testcycles = testcycles + 1
elif not extension_order[testcycles] in setthatneeds4:
if count>2:
#newtarget = [s[tmptargetA[1]-extendAseed -len(extensionA): leftbound], tmptargetA[1]-extendAseed -len(extensionA), leftbound, s[rightbound: tmptargetB[2]+extendBseed+ len(extensionB)], rightbound,tmptargetB[2]+extendBseed+ len(extensionB) ]
#print extension_order[testcycles]
#print "targetA, target B, extensionA, extentionB: {0}, {1}, {2}, {3}, {4}".format(tmptargetA, tmptargetB, extensionA, extensionB, testcycles)
#print "about to be returned : {0}, not in setthatneeds4".format(newtarget)
dashedA = str(newtarget[0][0:count-1])+(extendAseed)*'-'+ str(target[6])
dashedB = str(target[7])+extendBseed*'-'+ str(newtarget[3][-(count-1):])
newtarget.append(dashedA)
newtarget.append(dashedB)
#print dashedA
#print dashedB
#print newtarget
#print '\n'
return newtarget
return target
def controlpanel:
s_file = "ecoli_16s.txt"
seq=open(s_file, 'r')
s = seq.read().strip()
seq.close()
#s = [line.strip() for line in open(s_file, 'r')]
a = "arms.txt"
arms = [line.strip() for line in open(a, 'r')]
arms = listify(arms)
seeds = seedmake(arms, s)
#for seed in seeds:
# print seed
print len(seeds)
piece_maker(s,12)
controlpanel()