def hashAlignment():
objs = ''
new_black = True
ref_align = True
obj_count = 1
obj = classMAF.MAF(obj_count)
objs_list = [obj]
for line in open(ifile, 'r'):
line = line.strip()
if line == '':
obj_count += 1
ref_align = True
obj = classMAF.MAF(obj_count)
objs_list.append(obj)
else:
if not line.startswith('s '):
obj.addData(line)
else:
if ref_align == True:
obj.addRefAlign(line)
ref_align = False
else:
obj.addtargetAlign(line)
for ob in objs_list[:-1]:
print str(ob.RefChro()) + '\t'+ \
str(ob.RefStart()) + '\t'+ \
str(ob.RefEnd()) + '\t' + \
str(ob.TargetChro()) + '_'+ \
str(ob.TargetStart()) + '_'+ \
str(ob.TargetEnd()) + '_' + \
str(ob.TargetStrand()) + '\t' + \
str(ob.identity()) + '\t' + \
str(ob.RefStrand())
def hashAlignment(chrom, cds_coords, start):
objs = ''
new_black = True
ref_align = True
print_flag = False
obj_count=1
obj = classMAF.MAF(obj_count)
objs_list = [obj]
for line in open(align, 'r'):
line = line.strip()
if line == '':
obj_count += 1
ref_align = True
obj = classMAF.MAF(obj_count)
objs_list.append(obj)
else:
if not line.startswith('s '):
obj.addData(line)
else:
if ref_align == True:
obj.addRefAlign(line)
ref_align = False
else:
obj.addtargetAlign(line)
query = candidate+'_Lj\t'
target = candidate+'_Mt\t'
blocks = {}
align_coords={}
for ob in objs_list[:-1]:
if ob.RefChro() == chrom:
temp = ob.AlignHash()
if ob.RefStrand() == '+':
for i in range(len(temp)):
if (int(ob.RefStart()) + i) in cds_coords:
if len(blocks) > 1 and last_block_len != len(blocks):
query += str('-'*99)
target += str('-'*99)
print_flag = True
query += temp[i][0]
target += temp[i][1]
last_block_len = len(blocks)
blocks[ob] = ''
else:
print 'Error at line'
print str(obj)
sys.exit('Refernce strand is - ')
if print_flag == True:
print query
print target
def hashAlignment(chrom, cds_coords, o2):
objs = ''
new_black = True
ref_align = True
obj_count = 1
obj = classMAF.MAF(obj_count)
objs_list = [obj]
for line in open(align, 'r'):
line = line.strip()
if line == '':
obj_count += 1
ref_align = True
obj = classMAF.MAF(obj_count)
objs_list.append(obj)
else:
if not line.startswith('s '):
obj.addData(line)
else:
if ref_align == True:
obj.addRefAlign(line)
ref_align = False
else:
obj.addtargetAlign(line)
align_coords = {}
for ob in objs_list[:-1]:
if ob.RefChro() == chrom:
temp = ob.AlignHash()
if ob.RefStrand() == '+':
for i in range(len(temp)):
align_coords[int(ob.RefStart()) + i + 1] = temp[i + 1]
### print mismaches
if temp[i + 1][0] != temp[i + 1][1]:
if (int(ob.RefStart()) + i + 1) in cds_coords:
o2.write(ob.RefChro() + '\t' +
str(int(ob.RefStart()) + i + 1) + '\t' +
temp[i + 1][0] + '\t' + temp[i + 1][1] +
'\t' + 'True' + '\n')
else:
o2.write(ob.RefChro() + '\t' +
str(int(ob.RefStart()) + i + 1) + '\t' +
temp[i + 1][0] + '\t' + temp[i + 1][1] +
'\t' + 'False' + '\n')
else:
print 'Error at line'
print str(obj)
sys.exit('Refernce strand is - ')
return align_coords
def hashAlignment(chrom):
objs = ''
new_black = True
ref_align = True
print_flag = False
obj_count=1
obj = classMAF.MAF(obj_count)
objs_list = [obj]
for line in open(align, 'r'):
line = line.strip()
if line == '':
obj_count += 1
ref_align = True
obj = classMAF.MAF(obj_count)
objs_list.append(obj)
else:
if not line.startswith('s '):
obj.addData(line)
else:
if ref_align == True:
obj.addRefAlign(line)
ref_align = False
else:
obj.addtargetAlign(line)
### hash align coords
align_hash = {}
for ob in objs_list[:-1]:
if ob.RefChro() == chrom:
temp = ob.AlignHash()
if ob.RefStrand() == '+':
for i in range(len(temp)):
align_hash[int(ob.RefStart()) + i] = ''
else:
print 'Error at line'
print str(obj)
sys.exit('Refernce strand is - ')
return align_hash
def parseMAF():
o = open(ifile + '.nonRed', 'w')
if bed == True:
b = open(ifile + '.bed', 'w')
objs = ''
new_black = True
ref_align = True
obj_count = 1
obj = classMAF.MAF(obj_count)
objs_list = [obj]
for chrom in chro:
for line in open(ifile, 'r'):
line = line.strip()
if line == '':
obj_count += 1
ref_align = True
obj = classMAF.MAF(obj_count)
objs_list.append(obj)
else:
if not line.startswith('s '):
obj.addData(line)
else:
if ref_align == True:
obj.addRefAlign(line)
ref_align = False
else:
obj.addtargetAlign(line)
chr_obj_pos = {}
for ob in objs_list[:-1]:
if ob.RefChro() == chrom:
chr_obj_pos[int(ob.RefStart())] = ob
chr_obj = []
for key in sorted(chr_obj_pos):
chr_obj.append(chr_obj_pos[key])
hash_coords = {}
hash_coords_obj = {}
obj_list = {}
obj_count = 0
for obj in chr_obj:
obj_count += 1
if obj.RefChro() == chrom:
for i in range(int(obj.RefStart()), int(obj.RefEnd()) + 1, 1):
if i in hash_coords:
if hash_coords_obj[i].RefSize() > obj.RefSize():
if obj in obj_list:
del obj_list[obj]
break
else:
hash_coords[i] = obj.RefSize()
if hash_coords_obj[i] in obj_list:
del obj_list[hash_coords_obj[i]]
if obj not in obj_list:
obj_list[obj] = ''
hash_coords_obj[i] = obj
else:
hash_coords[i] = obj.RefSize()
if obj not in obj_list:
obj_list[obj] = ''
hash_coords_obj[i] = obj
print len(obj_list)
print chrom, '{:9,.0f}'.format(i)
print obj.TargetChro(), obj.TargetStart()
for ob in obj_list:
o.write(ob.Data() + '\n')
if bed == True:
b.write(ob.RefChro() + '\t' + str(ob.RefStart()) + '\t' +
str(ob.RefEnd()) + '\t' + ob.TargetChro() + '_' +
str(ob.TargetStart()) + '_' + str(ob.TargetEnd()) +
'\t' + str(ob.identity()) + '\t' +
str(ob.RefStrand()) + '\n')
o.close()
if bed == True:
b.close()