def test_make_trans(self):
"""make_trans should return trans table mapping chars to default"""
a = make_trans()
self.assertEqual('abc123'.translate(a), 'abc123')
a = make_trans('a', 'x')
self.assertEqual('abc123'.translate(a), 'xbc123')
a = make_trans('ac', 'xa')
self.assertEqual('abc123'.translate(a), 'xba123')
a = make_trans('ac', 'xa', '.')
self.assertEqual('abc123'.translate(a), 'x.a...')
self.assertRaises(ValueError, make_trans, 'ac', 'xa', 'av')
def test_make_trans(self):
"""make_trans should return trans table mapping chars to default"""
a = make_trans()
self.assertEqual("abc123".translate(a), "abc123")
a = make_trans("a", "x")
self.assertEqual("abc123".translate(a), "xbc123")
a = make_trans("ac", "xa")
self.assertEqual("abc123".translate(a), "xba123")
a = make_trans("ac", "xa", ".")
self.assertEqual("abc123".translate(a), "x.a...")
self.assertRaises(ValueError, make_trans, "ac", "xa", "av")
def test_make_trans(self):
"""make_trans should return trans table mapping chars to default"""
a = make_trans()
self.assertEqual('abc123'.translate(a), 'abc123')
a = make_trans('a', 'x')
self.assertEqual('abc123'.translate(a), 'xbc123')
a = make_trans('ac', 'xa')
self.assertEqual('abc123'.translate(a), 'xba123')
a = make_trans('ac', 'xa', '.')
self.assertEqual('abc123'.translate(a), 'x.a...')
self.assertRaises(ValueError, make_trans, 'ac', 'xa', 'av')
#!/usr/bin/env python
from cogent.struct.rna2d import ViennaStructure, wuss_to_vienna
from cogent.util.transform import make_trans
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.5.3-dev"
__maintainer__ = "Shandy Wikman"
__email__ = "*****@*****.**"
__status__ = "Development"
to_vienna_table = make_trans('><', '()')
def consan_parser(lines):
"""
Takes a series of lines as input.
Returns a list containing alignment and structure
ex: [{alignment},[structure]]
"""
seqs = []
struct = ''
pairs = []
alignment = {}
for line in lines:
if sequence(line):
line = line.split()
"""
mismatches = 0
if pairs is None:
try:
pairs = sequence.Alphabet.Pairs
except AttributeError:
pairs = sequence.Pairs
for up, down in self.directed():
curr = (sequence[up], sequence[down])
if curr not in pairs:
mismatches += 1
return mismatches
wuss_to_vienna_table = make_trans('<([{>)]} ', '(((()))) ', '.')
def wuss_to_vienna(data):
"""Converts WUSS format string to Vienna format.
Any pseudoknots or unrecognized chars will convert to unpaired bases.
Spaces will be preserved.
"""
return ViennaStructure(data.translate(wuss_to_vienna_table))
class StructureString(str):
"""Base class for ViennaStructure and WussStructure. Immutable.
StructureString holds a structure and a energy. By default energy is
set to None.
"""
mismatches = 0
if pairs is None:
try:
pairs = sequence.Alphabet.Pairs
except AttributeError:
pairs = sequence.Pairs
for up, down in self.directed():
curr = (sequence[up], sequence[down])
if curr not in pairs:
mismatches += 1
return mismatches
wuss_to_vienna_table = make_trans('<([{>)]} ', '(((()))) ', '.')
def wuss_to_vienna(data):
"""Converts WUSS format string to Vienna format.
Any pseudoknots or unrecognized chars will convert to unpaired bases.
Spaces will be preserved.
"""
return ViennaStructure(data.translate(wuss_to_vienna_table))
class StructureString(str):
"""Base class for ViennaStructure and WussStructure. Immutable.
StructureString holds a structure and a energy. By default energy is
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
primary_table = make_trans('{[]}','....')
first_table = make_trans('({[]})','..()..')
second_table = make_trans('([{}])','..()..')
def to_pairs(struct=None):
"""
Converts structure string in to a pairs object.
Starts by checking for pseudoknots if pseudoknotted it translates each
steam in to vienna notation and from there makes a pairs object.
Each pairs object is then joined to form the final pairs object of
the entire structure
Returns a tuple of the pairs object and the energy
"""
primary = first = second = struct.split(None,2)[0]
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
primary_table = make_trans('{[]}', '....')
first_table = make_trans('({[]})', '..()..')
second_table = make_trans('([{}])', '..()..')
def to_pairs(struct=None):
"""
Converts structure string in to a pairs object.
Starts by checking for pseudoknots if pseudoknotted it translates each
steam in to vienna notation and from there makes a pairs object.
Each pairs object is then joined to form the final pairs object of
the entire structure
Returns a tuple of the pairs object and the energy
"""
primary = first = second = struct.split(None, 2)[0]
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Shandy Wikman"
__email__ = "*****@*****.**"
__status__ = "Development"
def nupack_parser(lines=None,pseudo=True):
"""Parser for NUPACK output format
pseudo - If True pseudoknot will be keept if False it will be removed
"""
result = line_parser(lines,pseudo)
return result
curly_to_dots_table = make_trans('{}','..')
bracket_to_dots_table = make_trans('()','..')
curly_to_bracket_table = make_trans('{}','()')
def line_parser(lines=None,pseudo=True):
"""Parser for nupack output format
Returns list containing: sequence, paris and energy
ex: [[seq,[struct],energy]]
"""
record = False
result = []
SSEList = [] #Sequence,Structure,Energy
for line in lines:
if line.startswith('Error'):#Error no structure found
result = [Pairs([])] #return empty pairs list
#!/usr/bin/env python
from cogent.struct.rna2d import ViennaStructure,wuss_to_vienna
from cogent.util.transform import make_trans
__author__ = "Shandy Wikman"
__copyright__ = "Copyright 2007-2011, The Cogent Project"
__contributors__ = ["Shandy Wikman"]
__license__ = "GPL"
__version__ = "1.6.0dev"
__maintainer__ = "Shandy Wikman"
__email__ = "*****@*****.**"
__status__ = "Development"
to_vienna_table = make_trans('><','()')
def consan_parser(lines):
"""
Takes a series of lines as input.
Returns a list containing alignment and structure
ex: [{alignment},[structure]]
"""
seqs = []
struct = ''
pairs = []
alignment = {}
for line in lines:
if sequence(line):
line = line.split()
name = line[0].strip()
c = 0
tmp_seq = sline[-1]
seq = "".join([seq, tmp_seq])
elif c == 0: # struct line (every other line)
if line.startswith(name):
c = 1
tmp_struct = sline[-1]
struct = "".join([struct, tmp_struct])
struct, seq = remove_gaps(struct, seq)
pairs = convert_to_vienna(struct)
result.append([seq, pairs])
return result
cove_to_vienna_table = make_trans("><", "()")
def remove_gaps(struct, seq):
"""Remove gaps function
Some results comes with gaps that need to be removed
"""
seq = seq.replace("-", "")
tmp_struct = struct.split() # removes gaps
tmp = ""
for i in range(len(tmp_struct)):
tmp = "".join([tmp, tmp_struct[i]]) # put struct parts together
struct = tmp
if len(struct) != len(seq): # check so that struct and seq match in length
raise ValueError, "Sequence length don't match structure length"
