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 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 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 parse_residues(residue_lines, num_base, unpaired_symbol):
"""Return RnaSequence and Pairs object from residue lines.
residue_lines -- list of lines or anything that behaves like it.
Lines should contain:
residue_position, residue_identiy, residue_partner.
num_base -- int, basis of the residue numbering. In bpseq files from
the CRW website, the numbering starts at 1.
unpaired_symbol -- string, symbol in the 'partner' column that indicates
that a base is unpaired. In bpseq files from the CRW website, the
unpaired_symbol is '0'. This parameter should be a string to allow
other symbols that can't be casted to an integer to indicate
unpaired bases.
Checks for double entries both in the sequence and the structure, and
checks that the structre is valid in the sense that if (up,down) in there,
that (down,up) is the same.
"""
#create dictionary/list for sequence and structure
seq_dict = {}
pairs = Pairs()
for line in residue_lines:
try:
pos, res, partner = line.strip().split()
if partner == unpaired_symbol:
# adjust pos, not partner
pos = int(pos) - num_base
partner = None
else:
# adjust pos and partner
pos = int(pos) - num_base
partner = int(partner) - num_base
pairs.append((pos, partner))
#fill seq_dict
if pos in seq_dict:
raise BpseqParseError(\
"Double entry for residue %s (%s in bpseq file)"\
%(str(pos), str(pos+1)))
else:
seq_dict[pos] = res
except ValueError:
raise BpseqParseError("Failed to parse line: %s" % (line))
#check for conflicts, remove unpaired bases
if pairs.hasConflicts():
raise BpseqParseError("Conflicts in the list of basepairs")
pairs = pairs.directed()
pairs.sort()
# construct sequence from seq_dict
seq = RnaSequence(construct_sequence(seq_dict))
return seq, pairs
def parse_residues(residue_lines, num_base, unpaired_symbol):
"""Return RnaSequence and Pairs object from residue lines.
residue_lines -- list of lines or anything that behaves like it.
Lines should contain:
residue_position, residue_identiy, residue_partner.
num_base -- int, basis of the residue numbering. In bpseq files from
the CRW website, the numbering starts at 1.
unpaired_symbol -- string, symbol in the 'partner' column that indicates
that a base is unpaired. In bpseq files from the CRW website, the
unpaired_symbol is '0'. This parameter should be a string to allow
other symbols that can't be casted to an integer to indicate
unpaired bases.
Checks for double entries both in the sequence and the structure, and
checks that the structre is valid in the sense that if (up,down) in there,
that (down,up) is the same.
"""
#create dictionary/list for sequence and structure
seq_dict = {}
pairs = Pairs()
for line in residue_lines:
try:
pos, res, partner = line.strip().split()
if partner == unpaired_symbol:
# adjust pos, not partner
pos = int(pos) - num_base
partner = None
else:
# adjust pos and partner
pos = int(pos) - num_base
partner = int(partner) - num_base
pairs.append((pos,partner))
#fill seq_dict
if pos in seq_dict:
raise BpseqParseError(\
"Double entry for residue %s (%s in bpseq file)"\
%(str(pos), str(pos+1)))
else:
seq_dict[pos] = res
except ValueError:
raise BpseqParseError("Failed to parse line: %s"%(line))
#check for conflicts, remove unpaired bases
if pairs.hasConflicts():
raise BpseqParseError("Conflicts in the list of basepairs")
pairs = pairs.directed()
pairs.sort()
# construct sequence from seq_dict
seq = RnaSequence(construct_sequence(seq_dict))
return seq, pairs
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
