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globalAlign.py
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globalAlign.py
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import time, os
from Bio.SubsMat.MatrixInfo import blosum62 as blosum62
import mechanize
import re
# init calc
def initCalc(matrix,width,high,gap):
aux = 0
for i in xrange(high):
matrix[i][0] = aux
aux -= gap
aux = 0
for i in xrange(width):
matrix[0][i] = aux
aux -= gap
# init direction
def initDirection(direction,width,high):
direction[0][0] = "\033[1;32mnone\033[1;m"
for i in xrange(1,high):
direction[i][0] = "up"
for i in xrange(1,width):
direction[0][i] = "left"
# cell/direction calc
def cellCalc(matrix,direction,width,high,seq1,seq2,opt,gap):
calc = []
for i in xrange(1,high): #high
for j in xrange(1,width): #width
if opt==1: # ALTO
pair = (seq1[j],seq2[i])
calc.append(matrix[i-1][j]-gap) # UP 0
calc.append(matrix[i-1][j-1]+scoreMatch(pair,blosum62)) # DIAGONAL 1
calc.append(matrix[i][j-1]-gap) # LEFT 2
matrix[i][j] = max(calc)
if(calc.index(max(calc)) == 0):
direction[i][j] = "up"
if (calc.index(max(calc)) == 1):
direction[i][j] = "diag"
if(calc.index(max(calc)) == 2):
direction[i][j] = "left"
calc = []
if opt==2: # BAIXO
pair = (seq1[j],seq2[i])
calc.append(matrix[i][j-1]-gap) # LEFT 0
calc.append(matrix[i-1][j-1]+scoreMatch(pair,blosum62)) # DIAGONAL 1
calc.append(matrix[i-1][j]-gap) # UP 2
matrix[i][j] = max(calc)
if(calc.index(max(calc)) == 0):
direction[i][j] = "left"
if (calc.index(max(calc)) == 1):
direction[i][j] = "diag"
if(calc.index(max(calc)) == 2):
direction[i][j] = "up"
calc = []
def scoreMatch(pair,blosum62):
if pair not in blosum62:
return blosum62[(tuple(reversed(pair)))]
else:
return blosum62[pair]
def scorePairwise(alignX,alignY,blosum62,gap):
score = 0
for i in range(len(alignX)):
pair = (alignX[i], alignY[i])
if '-' in pair:
score -= gap
else:
score += scoreMatch(pair,blosum62)
return score
def globalAlign(matrix,direction,width,high,seq1,seq2,gap):
calc = []
path = "start"
alignX = ""
alignY = ""
i = high-1
j = width-1
while 1:
if(direction[i][j] == "up"):
path +=" up"
alignX += "-"
alignY += seq2[i]
direction[i][j] = "\033[1;32mup\033[1;m"
i = i-1
elif(direction[i][j] == "left"):
path += " left"
alignX += seq1[j]
alignY += "-"
direction[i][j] = "\033[1;32mleft\033[1;m"
j = j-1
elif(direction[i][j] == "diag"):
path += " diagonal"
alignX += seq1[j]
alignY += seq2[i]
direction[i][j] = "\033[1;32mdiag\033[1;m"
i = i-1
j = j-1
elif(i==0 or j==0):
break
print
alignX = alignX[::-1]
alignY = alignY[::-1]
lstX = [alignX[i:i+50] for i in range(0, len(alignX), 50)]
lstY = [alignY[i:i+50] for i in range(0, len(alignY), 50)]
score = scorePairwise(alignX, alignY, blosum62, gap)
print
print "Matrix: BLOSUM62"
print "Gap: "+str(gap)
print "Length: "+str(len(alignX))
print "Score: "+str(score)
print
for (lX,lY) in zip(lstX,lstY):
print "\t\t"+lX
print "\t\t"+lY
print
print
def needleAlign():
print "\t\t\t"+"--------------------"
print "\t\t\t"+"EBI GLOBAL ALIGNMENT"
print "\t\t\t"+"--------------------"
file1 = "protein1"
file2 = "protein2"
url = "http://www.ebi.ac.uk/Tools/services/web_emboss_needle/toolform.ebi"
br = mechanize.Browser()
br.set_handle_robots(False) # ignore robots
br.open(url)
br.select_form(predicate=lambda f: f.attrs.get('id', None) == 'jd_toolSubmissionForm')
br.set_all_readonly(False)
br.form.add_file(open(file1), 'text/plain', file1, name='aupfile')
br.form.add_file(open(file2), 'text/plain', file2, name='bupfile')
response = br.submit()
content = response.read()
with open("result", "w") as f:
f.write(content)
textfile = open("result", 'r')
filetext = textfile.read()
textfile.close()
lst = re.findall("(emboss_needle-(\w*\d*)-(\w*\d*)-(\w*\d*)-(\w*\d*)-(\w{2}))", filetext)
jobID = str(lst[0][0])
os.remove("result")
time.sleep(8)
url2 = "http://www.ebi.ac.uk/Tools/services/rest/emboss_needle/result/"+jobID+"/aln"
br.retrieve(url2,'data')[0]
with open("data", 'r') as fileIn:
print fileIn.read()
os.remove("data")
def stretcherAlign():
print "\t\t\t"+"--------------------"
print "\t\t\t"+"EBI GLOBAL ALIGNMENT"
print "\t\t\t"+"--------------------"
file1 = "protein1"
file2 = "protein2"
url = "http://www.ebi.ac.uk/Tools/services/web_emboss_stretcher/toolform.ebi"
br = mechanize.Browser()
br.set_handle_robots(False) # ignore robots
br.open(url)
br.select_form(predicate=lambda f: f.attrs.get('id', None) == 'jd_toolSubmissionForm')
br.set_all_readonly(False)
br.form.add_file(open(file1), 'text/plain', file1, name='aupfile')
br.form.add_file(open(file2), 'text/plain', file2, name='bupfile')
response = br.submit()
content = response.read()
with open("result", "w") as f:
f.write(content)
textfile = open("result", 'r')
filetext = textfile.read()
textfile.close()
lst = re.findall("(emboss_stretcher-(\w*\d*)-(\w*\d*)-(\w*\d*)-(\w*\d*)-(\w{2}))", filetext)
jobID = str(lst[0][0])
os.remove("result")
time.sleep(5)
url2 = "http://www.ebi.ac.uk/Tools/services/rest/emboss_stretcher/result/"+jobID+"/aln"
br.retrieve(url2,'data')[0]
with open("data", 'r') as fileIn:
print fileIn.read()
os.remove("data")
def main():
start = time.clock()
print "\t\t\t"+"----------------"
print "\t\t\t"+"GLOBAL ALIGNMENT"
print "\t\t\t"+"----------------"
seq1 = '-'
seq2 = '-'
gapOpen = 0
gapExtend = 0
gap = 0
try:
with open("protein1", "r") as f1:
seq1 += f1.read()
with open("protein2", "r") as f2:
seq2 += f2.read()
except IOError:
print "File doesn't exist !"
opt = input("Highroad = 1 or Lowroad = 2: ")
while 1:
if opt==1 or opt==2:
break
else:
opt = input("Wrong choice, please try again: ")
print
print "1 - EMBOSS Needle\n2 - EMBOSS Stretcher"
opt = input("Choose an EBI Alignment tool: ")
while 1:
if opt == 1:
gapOpen = 10
gapExtend = 0.5
gap = round((gapOpen*1+gapExtend*6)/7,0)+1
width = len(seq1)
high = len(seq2)
matrix = [[0 for x in xrange(width)] for x in xrange(high)]
direction = [[" " for x in xrange(width)] for x in xrange(high)]
# INIT & CALC
initCalc(matrix,width,high,gap)
initDirection(direction,width,high)
cellCalc(matrix,direction,width,high,seq1,seq2,opt,gap)
# GLOBAL ALIGN
globalAlign(matrix,direction,width,high,seq1,seq2,gap)
# EMBOSS NEEDLE
needleAlign()
end = time.clock()
print "Program Running Time: "+str(abs(start-end))+" seconds"
print
return
elif opt == 2:
gapOpen = 12
gapExtend = 2
gap = round((gapOpen*1+gapExtend*6)/7,0)+1
width = len(seq1)
high = len(seq2)
matrix = [[0 for x in xrange(width)] for x in xrange(high)]
direction = [[" " for x in xrange(width)] for x in xrange(high)]
# INIT & CALC
initCalc(matrix,width,high,gap)
initDirection(direction,width,high)
cellCalc(matrix,direction,width,high,seq1,seq2,opt,gap)
# GLOBAL ALIGN
globalAlign(matrix,direction,width,high,seq1,seq2,gap)
# EMBOSS STRETCHER
stretcherAlign()
end = time.clock()
print "Program Running Time: "+str(abs(start-end))+" seconds"
print
return
else:
print "Choose an EBI Alignment tool: ",
opt = input()