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arm_maker_3_24_15
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arm_maker_3_24_15
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#Step 1:
#Create list of potential arms which fall into realistic parameters of arms
##Current parameters:
##Hairpin minimum length = 4
##Hairpin maximum length = 16 (taken from 518 loop)
##Hairpins larger than 9nt long must be bridged with 6bps
##2bp long bridges can't bound hairpin loops of 5 or more nts
##
##
##Arms of less than 40 bp can't have more than 3 open loops per side
##Arms can't be composed of more than 40% unpaired nts (excluding hairpin unpaired nts)
#seq_file =
#"GGGGCCGTAGCTCAGCTGGGAGAGCACCTGCTTTGCAAGCAGGGGGTCGTCGGTTCGATCCCGTCCGGCTCCACCA"
#This one has 3bp long complement to find. Program will only fold
#4bp+ stretches now
#http://trna.bioinf.uni-leipzig.de/DataOutput/Result?ID=tdbD00003770
#alanine from Brucella melitensis
#seq_file = "GGGGGCUCUGUUGGUUCUCCCGCAACGCUACUCUGUUUACCAGGUCAGGUCCGGAAGGAAGCAGCCAAGGCAGAUGACGCGUGUGCCGGGAUGUAGCUGGCAGGGCCCCCACC"
#seq_file = 'GCCGGGCGCGGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCTAAGGAGGGGTGAACCGGCCCAGGTCGGAAACGGAGCAGGTCAAAACTCCCGTGCTGATCAGTAGTGGGATCGCGCCTGTGAATAGCCACTGCACTCCAGCCTGGGCAACATAGCGAG'
#http://www.ncbi.nlm.nih.gov/nuccore/527047183?report=fasta
#seq_file = "AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA"
#http://rna.ucsc.edu/rnacenter/xrna/xrna_gallery.html
#http://www.ebi.ac.uk/ena/data/view/A14565&display=fasta
#http://www.arb-silva.de/browser/ssu-121/silva/CP001368
#currently reliably(?) finding hairpin turn ends
#seq_file = "AAATTGAAGAGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGAAGCTTGCTTCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTGGTCTTGACATCCACGGAAGTTTTCAGAGATGAGAATGTGCCTTCGGGAACCGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTTGTGAAATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACGACCAGGGCTACACACGTGCTACAATGGCGCATACAAAGAGAAGCGACCTCGCGAGAGCAAGCGGACCTCATAAAGTGCGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTGGATCAGAATGCCACGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGTTGCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACTGGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTA" #
#seq_file = "GAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCT"
#seq_file = seq_file[0:500]
from Bio.Seq import Seq
from collections import defaultdict
# new strategy: get nuclei
# built out with Ns for shorter segments
# of the secondary folds, select the one closest to the ends of the primary fold
#true fold
#[['GAGTAAAG', 24, 32, 'CTTTGCTC', 39, 47], ['GCGGG', 11, 16, 'CCCGC', 57, 62], ['TTTC', 6, 10,
##def reduceloop(target, s): #functional
##
## #consider a formed helix as a single nt long position
## #also reduces full length of s so that only regions local to the existing fold are considered
## #s_reduced = s[0:target[1]+1] + "-" + s[target[5]:len(s) + 1]
## new_s = s[target[1]-12:target[1]] + "-" + s[target[5]:target[5]+12]
##
## s_reduced = new_s
## #print s[target[1]-25:target[5]+25]
## #return s_reduced
def piece_inhelix(target, s, size, extend): #make pieces in local regions surrounding a previously formed helix.
#it's not making pieces in the right places
lefthalf = []
righthalf=[]
pieces =[]
maxlen = len(s)
begin = target[1]-extend+1
leftmiddle = target[1]
rightmiddle = target[5]
end = target[5]+extend +2
if begin == leftmiddle:
return pieces
if rightmiddle + size >= end:
return pieces
if maxlen > end:
maxlen = end
length = leftmiddle-begin
j = begin
if j < 0 :
j = 0
while j <(leftmiddle-3):
piece = s[j:j+size]
if len(piece)<3:
break
else:
lefthalf.append([piece, j, j+size])
j = j + 1
j = rightmiddle
while j<(end-size):
piece = s[j:j+size]
if len(piece)<3:
break
else:
righthalf.append([piece, j, j+size])
j = j + 1
#print target
pieces = [lefthalf] + [righthalf]
#print pieces
return pieces
def target_extend_outwards2(target, s): # not used ever... get rid of?
#extend unbroken hairpin seeds that fall outside of the initial 32nt long segments(2 10nt matches+ 11nt max loop)
#add on outer end until hamming threshold is reached
#this will be a rare event
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]
hamm = 0
while hamm == 0:
tmptargetA = [s[targetA[1]-1:leftbound], targetA[1]-1, leftbound]
tmptargetB = [s[rightbound:targetB[2]+1], rightbound, targetB[2]+1]
hamm = rna_hamming(tmptargetA[0], tmptargetB[0])
if hamm!= 0:
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 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 == "N" or charB =="N" or charC == "N":
hamming = hamming + 0
else:
hamming = hamming + 1
return hamming
def seed_make(pieces, s): # working completely
targets =[]
#print str(pieces)
pieces_copy = pieces
for piece in pieces:
for piece_copy in pieces_copy:
if piece[2] < piece_copy[1] and 3<(piece_copy[1]-piece[2])<17:
#if piece[1] > seqlength:
# piece[1] = piece[1]-seqlength
if len(piece[0]) ==len(piece_copy[0]):
if rna_hamming(piece[0], piece_copy[0]) == 0:
range1=set(range(piece[1],piece[2]))
range2=set(range(piece_copy[1], piece_copy[2]))
if not range1.intersection(range2):
target = piece + piece_copy #the zero is the gap penalty
#print target
#print "target: {0}".format(target)
#print "before extend " + str(target)
target = target_extend_inwards(target, s)
#print "after inwards " + str(target)
target = target_extend_outwards(target, s)
#print "after outwards " + str(target)
if len(target[0])==2:
if (target[4]-target[2])>5: #2bp seeds can't bound large hairpin loops
continue
if (target[4]-target[2])>9:
if len(target[0])<4:
continue
if (target[4]-target[2])>12:
if len(target[0])<6:
continue
#print "after outwards " + str(target)
if not target in targets:
target.append(target[0])
target.append(target[3])
targets.append(target)
#
return targets
def piece_maker(s, size): #used to fragment sequence
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 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]
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], tmptargetB[0])
if hamm!= 0:
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] < 4: # this is never happening
print "target already less than 4"
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]) > 4:
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]) < 4:
return (targetA + targetB)
else:
targetA=tmptargetA
targetB = tmptargetB
#print "end targeta {0}, and targetB {1}".format(targetA, targetB)
return (targetA + targetB )
def target_extend(target,s, order): #index tracking is off on both sides, but offsets are working.
#print "enter closerange"
#print "target: {0}".format(target)
#maybe a combination of pieces_inhelix and target_extend?
#target extend is not finding the double internal loop at 436.
# but pieces inhelix can
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 == "short":
extension_order = ['00', '10', '01', '11', '21', '12', '02', '20', '22']#, '03', '30', '31', '13', '23', '32', '33', '42', '24','04', '40', '42', '24', '43', '34', '44', '52', '25', '53', '35', '05', '50', '06', '60', '54', '45', '55', '63', '36', '64', '46', '65', '56', '66', '74', '47', '75', '57', '76', '67', '77', '87', '78', '88', '89', '98', '99']
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
#return (tmptargetA + tmptargetB)
def end_arm_extension(target, s):
#print "enter closerange"
#print "target: {0}".format(target)
if target[1] <= 1:
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 = ['11']
while testcycles <1:
#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>1:
#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
return target
def small_hairpin_extension(target, s):
#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 = [ '00', '20', '02','01', '11', '11','12', '21'] #rearranged. May have to just break it up and run several times
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>1: #wrong here?
#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
return target
def remove_duplicates(targets):
s = []
for i in targets:
if i not in s:
s.append(i)
return s
#s1 = "AAATAAAGAAA"
#s2 = "TTTTTTTATTT"
#print len(s)
folds = defaultdict(list)
def trim_arms(arms):
trimmedarms=[]
print len(arms)
for arm in arms:
armlength = arm[2]-arm[1]
dashcount = arm[6].count("-")
if (1.00*dashcount/armlength)<.45: #arms can't be more than 40% unbonded bases
## print "arm6dashes {0}".format(arm[6].count("-"))
## print "dashcount/armlength+ {0}".format(1.00*dashcount/armlength)
## print arm
armlength = arm[5]-arm[4]
dashcount = arm[7].count("-")
if (1.00*dashcount/armlength)<.45: #arms can't be more than 45% unbonded bases#SO FAR most found is 40%
trimmedarms.append(arm)
print len(trimmedarms)
prevstate=""
unpaired_count = 0
more_trimmedarms=[]
for arm in trimmedarms:
prevstate=""
unpaired_count = 0
for char in arm[6]:
state = char
if char == "-" and prevstate != "-":
unpaired_count = unpaired_count + 1
prevstate = state
## print arm
## print unpaired_count
## print '\n'
if len(arm[0])<40 and unpaired_count<4:
prevstate=""
unpaired_count = 0
for char in arm[7]:
state = char
if char == "-" and prevstate != "-":
unpaired_count = unpaired_count + 1
prevstate = state
## print arm
## print unpaired_count
## print '\n'
if len(arm[3])<40 and unpaired_count<4:
more_trimmedarms.append(arm)
print len(more_trimmedarms)
return more_trimmedarms
def controlpanel(s):
#print rna_hamming(s1,s2)
pieces = piece_maker(s,2)
arms = []
groupkey = 0
seckey = 0
trikey = 0
groupdict= {}
secdict={}
tridict = {}
targets = []
seeds = seed_make(pieces, s)
#After each extension, the target is tried in close and long extend patterns
for seed in seeds:
#print seed
seedtargets = []
seedtargets.append(seed)
#print seedtargets
##############
if len(seed[0])==2: # short hairpin bounders must extend, or else they get thrown out
#print "seed {0}".format(seed)
extra = small_hairpin_extension(seed, s)
#print "extra : " +str(extra)
#print "extra {0}".format(extra)
#print "\n"
if extra == seed:
continue #if there's no close extension on top of 2 bp, the go to next seed
##if not (len(extra[0])==4 and len(extra[3])==4): #forgot what this is for...
if len(extra[0]) < 6:#to make sure arm extend enough in most cases
continue
else:
seed = extra
seedtargets.append(extra)
#print "extended seed: {0}".format(seed)
###############
seedtargets = remove_duplicates(seedtargets)
#print "\n"
#print seedtargets
i = 0
while i < 4:
tmpseedtargets = []
for seedtarget in seedtargets:
## print seedtarget
## print seedtargets
tmpseedtargets = tmpseedtargets + [target_extend(seedtarget, s, "short")]
#print "got here"
tmpseedtargets = tmpseedtargets + [end_arm_extension(seedtarget, s)]
seedtargets = seedtargets + tmpseedtargets
seedtargets = remove_duplicates(seedtargets)
i = i + 1
for seedtarget in seedtargets:
arms.append(seedtarget)
targets = []
arms = remove_duplicates(arms)
arms = trim_arms(arms)
return arms
s_file = "ecoli_16s.txt"
seq=open(s_file, 'r')
s = seq.read().strip()
seq.close()
#s=s[403:554]
#print "full sequence: " + str(s) + "\n"
#s = s[130:200]
#print "Partial sequence s[142:220]: {0}".format(s)
#print "\n"
#s=s[495:550]
#print s[25:37]
#print len(s)
arms = controlpanel(s)
a = "true_arms.txt"
true_arms = [line.strip() for line in open(a, 'r')]
truearms = []
for arm in true_arms:
newarm = eval(arm)
truearms.append(newarm)
##print '\n'
##print truearms
##print '\n'
##print arms
print [i for i in arms if i in truearms]
f = open("arms.txt", "w")
for arm in arms:
f.write("%s\n" % arm)
f.close()
print "done"
#print "s[1490: 1540]" + str(s[1490:1540])
#print "s[79:90]" + str(s[79:90])
#print "s[149:160]" + str(s[149:160])
#print "s[249:260]" + str(s[249:260])
#print "s[1439:1460]" + str(s[1439:1460])
#next: build dictionary FF:SF:TF
#STRUCTURE INDEX = 1, PROGRAM INDEX = 0
#right half matches structure numbering
#left half matches structure numbering -1
#Program architecture rewrite:
#extend in a pattern. 10 01 11 21 12 02 20 22 03 30 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
#as you get higher , you need a longer bridge at the end
# for 1 1 just need a 1 brdige
# for up to 2, need 2 bridge, not AT TA
#for three just need 2 bridge
# for 5 even, just need a 2 bridge
#determine rules for necessaary bridges.