def comRNA_parser(lines=None,pseudo=True,first=False):
"""Parsed comRNA output.
pseudo - if True, report results with pseudoknots; if flag
is False pseudoknots will be removed.
"""
names = get_names(lines)
result = []
for block in minimalComrnaParser(lines):
for structure in blockParser(block):
for struct in structParser(structure):
for pairs,seq in pairsParser(struct,names):
result.append([seq,pairs])
if first:
break
if first:
break
if first:
break
if not pseudo:
tmp = []
for block in result:
tmp.append([block[0],opt_single_random(block[-1])])
result = tmp
return result
def comRNA_parser(lines=None,pseudo=True,first=False):
"""Parsed comRNA output.
pseudo - if True, report results with pseudoknots; if flag
is False pseudoknots will be removed.
"""
names = get_names(lines)
result = []
for block in minimalComrnaParser(lines):
for structure in blockParser(block):
for struct in structParser(structure):
for pairs,seq in pairsParser(struct,names):
result.append([seq,pairs])
if first:
break
if first:
break
if first:
break
if not pseudo:
tmp = []
for block in result:
tmp.append([block[0],opt_single_random(block[-1])])
result = tmp
return result
def to_pairs(list=None,pseudo=True):
"""
Converts nupack structure string into pairs object
pseudoknotted and not pseudoknotted.
"""
tmp = list[1]
pairs = []
if list.__contains__('pseudoknotted!'):
#since pseudoknotted is denoted by {} it divides into {} and () string
#they are then turned into pairs lists seperatly and then the lists are
#joined to form the complete set of pairs
first = second = tmp
first = ViennaStructure(first.translate(curly_to_dots_table))
second = second.translate(bracket_to_dots_table)
second = ViennaStructure(second.translate(curly_to_bracket_table))
pairs = first.toPairs()
pairs.extend(second.toPairs())
pairs.sort()
if not pseudo:
pairs = opt_single_random(pairs)
pairs.sort()
else:
structure = ViennaStructure(tmp.translate(curly_to_bracket_table))
pairs = structure.toPairs()
pairs.sort()
return pairs
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
def pknotsrg_parser(lines=None,pseudo=True):
"""Parser for pknotsrg output format
Returns a list containing: sequence, structure and energy
ex: [[seq,[structure],energy]]
pseudo - If True pairs will be returned with pseudoknots
If False pairs will be returned without pseudoknots
"""
result = []
struct = str(lines[1]).strip('\n')
seq = lines[0].strip()
tmp_pairs,energy = to_pairs(struct)
tmp_pairs.sort()
if not pseudo:
tmp_pairs = opt_single_random(tmp_pairs)
tmp_pairs.sort()
result.append([seq,tmp_pairs,energy])
return result
def pknotsrg_parser(lines=None, pseudo=True):
"""Parser for pknotsrg output format
Returns a list containing: sequence, structure and energy
ex: [[seq,[structure],energy]]
pseudo - If True pairs will be returned with pseudoknots
If False pairs will be returned without pseudoknots
"""
result = []
struct = str(lines[1]).strip('\n')
seq = lines[0].strip()
tmp_pairs, energy = to_pairs(struct)
tmp_pairs.sort()
if not pseudo:
tmp_pairs = opt_single_random(tmp_pairs)
tmp_pairs.sort()
result.append([seq, tmp_pairs, energy])
return result
