def test_adjust_base_None(self):
"""adjust_base: should keep Nones or duplicates, ignore conflicts"""
pairs = Pairs([(2,8),(3,7),(6,None),(None,None),(2,10)])
expected = Pairs([(1,7),(2,6),(5,None),(None, None),(1,9)])
self.assertEqual(adjust_base(pairs,-1), expected)
p = Pairs([(1,2),(2,1),(1,2),(2,None)])
self.assertEqual(adjust_base(p, 1), [(2,3),(3,2),(2,3),(3,None)])
def ct_parser(lines=None):
"""Ct format parser
Takes lines from a ct file as input
Returns a list containing sequence,structure and if available the energy.
[[seq1,[struct1],energy1],[seq2,[struct2],energy2],...]
"""
count = 0
length = ''
energy = None
seq = ''
struct = []
result = []
for line in lines:
count+=1
sline = line.split(None,6) #sline = split line
if count==1 or new_struct(line):#first line or new struct line.
if count > 1:
struct = adjust_base(struct,-1)
struct = Pairs(struct).directed()
struct.sort()
if energy is not None:
result.append([seq,struct,energy])
energy = None
else:
result.append([seq,pairs])
struct = []
seq = ''
#checks if energy for predicted struct is given
if sline.__contains__('dG') or sline.__contains__('ENERGY'):
energy = atof(sline[3])
if sline.__contains__('Structure'):
energy = atof(sline[2])
else:
seq = ''.join([seq,sline[1]])
if not int(sline[4]) == 0:#unpaired base
pair = ( int(sline[0]),int(sline[4]) )
struct.append(pair)
#structs are one(1) based, adjust to zero based
struct = adjust_base(struct,-1)
struct = Pairs(struct).directed()
struct.sort()
if energy is not None:
result.append([seq,struct,energy])
else:
result.append([seq,struct])
return result
def ct_parser(lines=None):
"""Ct format parser
Takes lines from a ct file as input
Returns a list containing sequence,structure and if available the energy.
[[seq1,[struct1],energy1],[seq2,[struct2],energy2],...]
"""
count = 0
length = ''
energy = None
seq = ''
struct = []
result = []
for line in lines:
count+=1
sline = line.split(None,6) #sline = split line
if count==1 or new_struct(line):#first line or new struct line.
if count > 1:
struct = adjust_base(struct,-1)
struct = Pairs(struct).directed()
struct.sort()
if energy is not None:
result.append([seq,struct,energy])
energy = None
else:
result.append([seq,pairs])
struct = []
seq = ''
#checks if energy for predicted struct is given
if sline.__contains__('dG') or sline.__contains__('ENERGY'):
energy = atof(sline[3])
if sline.__contains__('Structure'):
energy = atof(sline[2])
else:
seq = ''.join([seq,sline[1]])
if not int(sline[4]) == 0:#unpaired base
pair = ( int(sline[0]),int(sline[4]) )
struct.append(pair)
#structs are one(1) based, adjust to zero based
struct = adjust_base(struct,-1)
struct = Pairs(struct).directed()
struct.sort()
if energy is not None:
result.append([seq,struct,energy])
else:
result.append([seq,struct])
return result
def column_parser(lines):
"""Parser column format"""
record = False
result = []
struct = []
seq = ''
for line in lines:
if line.startswith('; ------'): #structure part beginns
record = True
continue
if line.startswith('; ******'): #structure part ends
record = False
struct = adjust_base(struct,-1)
struct = Pairs(struct).directed()#remove duplicates
struct.sort()
result.append([seq,struct])
struct = []
seq = ''
continue
if record:
sline = line.split()
if sline[4] == '.': #skip not paired
seq = ''.join([seq,sline[1]])
continue
seq = ''.join([seq,sline[1]])
pair = (int(sline[3]),int(sline[4])) #(alignpos,align_bp)
struct.append(pair)
return result
def test_adjust_base(self):
"""adjust_base: should work for pairs object or list of pairs"""
p = Pairs()
self.assertEqual(adjust_base(p, 10), [])
pairs = [(1, 21), (2, 15), (3, 13), (4, 11), (5, 10), (6, 9)]
offset = -1
expected = [(0, 20), (1, 14), (2, 12), (3, 10), (4, 9), (5, 8)]
obs_pairs = adjust_base(pairs, offset)
self.assertEqual(obs_pairs, expected)
pairs = Pairs([(0, 10), (1, 9)])
self.assertEqual(adjust_base(pairs, -1), Pairs([(-1, 9), (0, 8)]))
self.assertEqual(adjust_base(pairs, 5), Pairs([(5, 15), (6, 14)]))
self.assertRaises(PairsAdjustmentError, adjust_base, pairs, 3.5)
def column_parser(lines):
"""Parser column format"""
record = False
result = []
struct = []
seq = ''
for line in lines:
if line.startswith('; ------'): #structure part beginns
record = True
continue
if line.startswith('; ******'): #structure part ends
record = False
struct = adjust_base(struct, -1)
struct = Pairs(struct).directed() #remove duplicates
struct.sort()
result.append([seq, struct])
struct = []
seq = ''
continue
if record:
sline = line.split()
if sline[4] == '.': #skip not paired
seq = ''.join([seq, sline[1]])
continue
seq = ''.join([seq, sline[1]])
pair = (int(sline[3]), int(sline[4])) #(alignpos,align_bp)
struct.append(pair)
return result
def test_adjust_base(self):
"""adjust_base: should work for pairs object or list of pairs"""
p = Pairs()
self.assertEqual(adjust_base(p,10),[])
pairs = [(1,21),(2,15),(3,13),(4,11),(5,10),(6,9)]
offset = -1
expected = [(0,20),(1,14),(2,12),(3,10),(4,9),(5,8)]
obs_pairs = adjust_base(pairs, offset)
self.assertEqual(obs_pairs, expected)
pairs = Pairs([(0,10),(1,9)])
self.assertEqual(adjust_base(pairs, -1), Pairs([(-1,9),(0,8)]))
self.assertEqual(adjust_base(pairs, 5), Pairs([(5,15),(6,14)]))
self.assertRaises(PairsAdjustmentError, adjust_base, pairs, 3.5)
def ilm_parser(lines=None, pseudo=True):
"""Ilm format parser
Takes lines as input and returns a list with Pairs object.
Pseudo - if True returns pairs with possible pseudoknot
if False removes pseudoknots
"""
pairs = []
for line in lines:
if line.startswith('Final') or len(line) == 1: #skip these lines
continue
line = line.strip('\n')
line = map(int, line.split(None, 2))
if line[1] == 0:
continue #Skip this line, not a pair
else:
pairs.append(line)
pairs = adjust_base(pairs, -1)
tmp = Pairs(pairs).directed()
tmp.sort()
if not pseudo:
tmp = opt_single_random(tmp)
tmp.sort()
result = []
result.append(tmp)
return result
def ilm_parser(lines=None,pseudo=True):
"""Ilm format parser
Takes lines as input and returns a list with Pairs object.
Pseudo - if True returns pairs with possible pseudoknot
if False removes pseudoknots
"""
pairs = []
for line in lines:
if line.startswith('Final') or len(line)==1:#skip these lines
continue
line = line.strip('\n')
line = map(int,line.split(None,2))
if line[1] == 0:
continue #Skip this line, not a pair
else:
pairs.append(line)
pairs = adjust_base(pairs,-1)
tmp = Pairs(pairs).directed()
tmp.sort()
if not pseudo:
tmp = opt_single_random(tmp)
tmp.sort()
result = []
result.append(tmp)
return result
