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rnahamming3_14_15_sequential
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#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 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 piece_maker(s, size): #working
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
return pieces
def target_extend_outwards(target, s):
#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:
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:
return (targetA + targetB)
else:
targetA=tmptargetA
targetB = tmptargetB
if (targetB[1] - targetA[2]) == 3:
#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_outwards2(target, s):
#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 closerange_target_extend(target,s): #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
extension_order = [00, 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]
while testcycles <len(extension_order):
hamm = 0
extensionA= ""
extensionB= ""
extend = 1
extendAseed = extension_order[testcycles][0]
extendBseed = extension_order[testcycles][1]
count = 0
##print "enterhamming loop"
print extension_order[testcycles]
while hamm == 0:
current_gap = gap + max(extension_order[testcycles][0], extension_order[testcycles][1])
#newtarget line index tracking is the problem. is the problem"? Roiund three starting one early
newtarget = [s[tmptargetA[1]-len(extensionA): leftbound], tmptargetA[1]-len(extensionA), leftbound, s[rightbound: tmptargetB[2]+ len(extensionB)], rightbound,tmptargetB[2]+len(extensionB), current_gap]
#print "running..." + str(count)
extensionA = s[tmptargetA[1]-extendAseed-extend:tmptargetA[1]]
extensionB = s[tmptargetB[2]:tmptargetB[2]+extendBseed+extend]
#something is off with checking for matches...figure out next
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
if count<3: #the new indexing is off
testcycles = testcycles + 1
elif 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}".format(newtarget)
return newtarget
return target
#return (tmptargetA + tmptargetB)
##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 exclude_match(targets):
mindistance = 100
target = []
for candidate in targets:
current_distance = candidate[4]-candidate[2]
if current_distance < mindistance:
mindistance = current_distance
target = [candidate]
return target
def piece_match2(pieces):
targets =[]
print pieces
if pieces:
lefthalf = pieces[0]
righthalf = pieces [1]
for left in lefthalf:
for right in righthalf:
if len(left[0]) ==len(right[0]):
if rna_hamming(left[0], right[0]) == 0:
target = left + right
print target
print "extend out"
target = target_extend_outwards(target, s) #FIX HERE#it's not extending far enough?
#pair matching is off. Need to redo architecture to add on one base at a time,...
print target
targets.append(target)
target = exclude_match(targets)
return target
def piece_match(pieces, s):
targets =[]
#print str(pieces)
pieces_copy = pieces
for piece in pieces:
for piece_copy in pieces_copy:
if piece[2] < piece_copy[1] and 4<(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: {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)
#print "after outwards " + str(target)
if not target in targets:
#print "closetarget round 1 for {0}".format(target)
#close_target = closerange_target_extend(target, s)
#print "close_target after round 1: {0}".format(close_target)
#print "closetarget round 2 for {0}".format(close_target)
#print "target after round 2: {0}".format(close_target2)
#print "target after round 3: {0}".format(close_target3)
#print "target after round 3: {0}".format(close_target4)
#print "\n"
#print "after nondup " + str(targets) + " "
targets.append(target)
## close_target = closerange_target_extend(target, s)
## if not close_target in targets:
## targets.append(close_target)
## close_target2 = closerange_target_extend(close_target, s)
## if not close_target2 in targets:
## targets.append(close_target2)
## close_target3 = closerange_target_extend(close_target2, s)
## if not close_target3 in targets:
## targets.append(close_target3)
## close_target4 = closerange_target_extend(close_target3, s)
## if not close_target4 in targets:
## targets.append(close_target4)
return targets
#hairpin loop size fine for now
#s1 = "AAATAAAGAAA"
#s2 = "TTTTTTTATTT"
s=seq_file
print len(s)
folds = defaultdict(list)
def controlpanel(s):
#print rna_hamming(s1,s2)
pieces = piece_maker(s,3)
arms = []
#altarms = []
#folddict1 = {}
#folddict2 ={}
#folddict3={}
groupkey = 0
seckey = 0
trikey = 0
groupdict= {}
secdict={}
tridict = {}
#inhelix_pieces =[]
redtargets = piece_match(pieces, s)
print "reduced target list len: {0}".format(len(redtargets))
for group in redtargets:
print group
groupkey = groupkey + 1
#group = target_extend_outwards2(group, s)
#print reduceloop(group, s)
#print "FIRST FOLD"
#print group
#print inhelix_pieces
inhelix_pieces = piece_inhelix(group, s, 4, 15)
#inhelix_pieces.append(piece_inhelix(group, s, 3, 12)) #extension may be broken?
#print inhelix_pieces
if inhelix_pieces:
sectargets = piece_match2(inhelix_pieces)
#groupdict[groupkey] = group
#altarms.append([groupkey])
#print group
arms.append([group, 0, 0])
for secgroup in sectargets:
#seckey = seckey +1
secgroup = target_extend_outwards2(secgroup, s)
#print reduceloop(secgroup, s)
#print "SECOND FOLD"
#print secgroup
inhelix_pieces = piece_inhelix(secgroup, s, 3, 12)
#altarms.append([groupkey, seckey])
arms.append([group, secgroup, 0])
#secdict[seckey] = secgroup
tritargets = piece_match2(inhelix_pieces)
for trigroup in tritargets:
#trikey = trikey + 1
#altarms.append([groupkey, seckey, trikey])
arms.append([group, secgroup, trigroup])
## #tridict[trikey] = trigroup
## #print "THIRD FOLD"
## #print thrgroup
## inhelix_pieces = piece_inhelix(trigroup, s, 3, 12)
## quadtargets = piece_match2(inhelix_pieces)
## for quadgroup in quadtargets:
## arms.append([group, secgroup, trigroup, quadgroup, 0])
## inhelix_pieces = piece_inhelix(quadgroup, s, 3, 12)
## quinttargets = piece_match2(inhelix_pieces)
## for quintgroup in quinttargets:
## arms.append([group, secgroup, trigroup, quadgroup, quintgroup])
##
for arm in arms:
print arm
#print arm
# print len(arms)
##
#print len(redtargets) #only 82 target seed for the 16s 28 arms
#need to get an accurate structure and sequence of a 16s
#print len(redtargets)
#s1 = "AAATAAAGAAA"
#s2 = "TTTTTTTATTT"
s=seq_file
s=s[403:554]
#print s[25:37]
print len(s)
controlpanel(s)
#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])
#AAATTGAAGAGTTTGATCATGGCTCAGATT
#AAAUUGAAGAGUUUGAUCAUGGCUCAGAUU
#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.