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import string, array
import Alphabet
from Alphabet import IUPAC
from Data.IUPACData import ambiguous_dna_complement, ambiguous_rna_complement
from Bio.Data import CodonTable
class Seq:
def __init__(self, data, alphabet = Alphabet.generic_alphabet):
# Enforce string storage
assert (type(data) == type("") or # must use a string
type(data) == type(u"")) # but can be a unicode string
self.data = data # Seq API requirement
self.alphabet = alphabet # Seq API requirement
def __repr__(self):
return "%s(%s, %s)" % (self.__class__.__name__,
repr(self.data),
repr(self.alphabet))
def __str__(self):
if len(self.data) > 60:
s = repr(self.data[:60] + " ...")
else:
s = repr(self.data)
return "%s(%s, %s)" % (self.__class__.__name__, s,
repr(self.alphabet))
# I don't think I like this method...
## def __cmp__(self, other):
## if isinstance(other, Seq):
## return cmp(self.data, other.data)
## else:
## return cmp(self.data, other)
def __len__(self): return len(self.data) # Seq API requirement
def __getitem__(self, i): return self.data[i] # Seq API requirement
def __getslice__(self, i, j): # Seq API requirement
i = max(i, 0); j = max(j, 0)
return Seq(self.data[i:j], self.alphabet)
def __add__(self, other):
if type(other) == type(' '):
return self.__class__(self.data + other, self.alphabet)
elif self.alphabet.contains(other.alphabet):
return self.__class__(self.data + other.data, self.alphabet)
elif other.alphabet.contains(self.alphabet):
return self.__class__(self.data + other.data, other.alphabet)
else:
raise TypeError, ("incompatable alphabets", str(self.alphabet),
str(other.alphabet))
def __radd__(self, other):
if self.alphabet.contains(other.alphabet):
return self.__class__(other.data + self.data, self.alphabet)
elif other.alphabet.contains(self.alphabet):
return self.__class__(other.data + self.data, other.alphabet)
else:
raise TypeError, ("incompatable alphabets", str(self.alphabet),
str(other.alphabet))
def tostring(self): # Seq API requirement
return self.data
def tomutable(self): # Needed? Or use a function?
return MutableSeq(self.data, self.alphabet)
def count(self, item):
return len([x for x in self.data if x == item])
def __maketrans(self, alphabet) :
"""Seq.__maketrans(alphabet) -> translation table.
Return a translation table for use with complement()
and reverse_complement().
Compatible with lower case and upper case sequences.
alphabet is a dictionary as implement in Data.IUPACData
For internal use only.
"""
before = ''.join(alphabet.keys())
after = ''.join(alphabet.values())
before = before + before.lower()
after = after + after.lower()
return string.maketrans(before, after)
def complement(self):
"""Returns the complement sequence. New Seq object.
"""
if self.alphabet in (IUPAC.ambiguous_dna, IUPAC.unambiguous_dna):
d = ambiguous_dna_complement
elif self.alphabet in (IUPAC.ambiguous_rna, IUPAC.unambiguous_rna):
d = ambiguous_rna_complement
elif 'U' in self.data:
d = ambiguous_rna_complement
else:
d = ambiguous_dna_complement
ttable = self.__maketrans(d)
#Much faster on really long sequences than the previous loop based one.
#thx to Michael Palmer, University of Waterloo
s = self.data.translate(ttable)
return Seq(s, self.alphabet)
def reverse_complement(self):
"""Returns the reverse complement sequence. new Seq object.
"""
if self.alphabet in (IUPAC.ambiguous_dna, IUPAC.unambiguous_dna):
d = ambiguous_dna_complement
elif self.alphabet in (IUPAC.ambiguous_rna, IUPAC.unambiguous_rna):
d = ambiguous_rna_complement
elif 'U' in self.data:
d = ambiguous_rna_complement
else:
d = ambiguous_dna_complement
ttable = self.__maketrans(d)
#Much faster on really long sequences than the previous loop based one.
#thx to Michael Palmer, University of Waterloo
s = self.data[-1::-1].translate(ttable)
return Seq(s, self.alphabet)
class MutableSeq:
def __init__(self, data, alphabet = Alphabet.generic_alphabet):
if type(data) == type(""):
self.data = array.array("c", data)
else:
self.data = data # assumes the input is an array
self.alphabet = alphabet
def __repr__(self):
return "%s(%s, %s)" % (self.__class__.__name__,
repr(self.data),
repr(self.alphabet))
def __str__(self):
if len(self.data) > 60:
s = repr(string.join(self.data[:60], "") + " ...")
else:
s = repr(string.join(self.data, ""))
return "%s(%s, %s)" % (self.__class__.__name__, s,
repr(self.alphabet))
def __cmp__(self, other):
if isinstance(other, MutableSeq):
x = cmp(self.alphabet, other.alphabet)
if x == 0:
return cmp(self.data, other.data)
return x
elif type(other) == type(""):
return cmp(self.data.tostring(), other)
elif isinstance(other, Seq):
x = cmp(self.alphabet, other.alphabet)
if x == 0:
return cmp(self.data.tostring(), other.data)
return x
else:
return cmp(self.data, other)
def __len__(self): return len(self.data)
def __getitem__(self, i): return self.data[i]
def __setitem__(self, i, item): self.data[i] = item
def __delitem__(self, i): del self.data[i]
def __getslice__(self, i, j):
i = max(i, 0); j = max(j, 0)
return self.__class__(self.data[i:j], self.alphabet)
def __setslice__(self, i, j, other):
i = max(i, 0); j = max(j, 0)
if isinstance(other, MutableSeq):
self.data[i:j] = other.data
elif isinstance(other, type(self.data)):
self.data[i:j] = other
else:
self.data[i:j] = array.array("c", str(other))
def __delslice__(self, i, j):
i = max(i, 0); j = max(j, 0)
del self.data[i:j]
def __add__(self, other):
if self.alphabet.contains(other.alphabet):
return self.__class__(self.data + other.data, self.alphabet)
elif other.alphabet.contains(self.alphabet):
return self.__class__(self.data + other.data, other.alphabet)
else:
raise TypeError, ("incompatable alphabets", str(self.alphabet),
str(other.alphabet))
def __radd__(self, other):
if self.alphabet.contains(other.alphabet):
return self.__class__(other.data + self.data, self.alphabet)
elif other.alphabet.contains(self.alphabet):
return self.__class__(other.data + self.data, other.alphabet)
else:
raise TypeError, ("incompatable alphabets", str(self.alphabet),
str(other.alphabet))
def append(self, c):
self.data.append(c)
def insert(self, i, c):
self.data.insert(i, c)
def pop(self, i = (-1)):
c = self.data[i]
del self.data[i]
return c
def remove(self, item):
for i in range(len(self.data)):
if self.data[i] == item:
del self.data[i]
return
raise ValueError, "MutableSeq.remove(x): x not in list"
def count(self, item):
count = 0
for c in self.data:
if c == item:
count = count + 1
return count
def index(self, item):
for i in range(len(self.data)):
if self.data[i] == item:
return i
raise ValueError, "MutableSeq.index(x): x not in list"
def reverse(self):
self.data.reverse()
def complement(self):
if self.alphabet in (IUPAC.ambiguous_dna, IUPAC.unambiguous_dna):
d = ambiguous_dna_complement
elif self.alphabet in (IUPAC.ambiguous_rna, IUPAC.unambiguous_rna):
d = ambiguous_rna_complement
elif 'U' in self.data:
d = ambiguous_rna_complement
else:
d = ambiguous_dna_complement
c = dict([(x.lower(), y.lower()) for x,y in d.iteritems()])
d.update(c)
self.data = map(lambda c: d[c], self.data)
self.data = array.array('c', self.data)
def reverse_complement(self):
self.complement()
self.data.reverse()
## Sorting a sequence makes no sense.
# def sort(self, *args): self.data.sort(*args)
def extend(self, other):
if isinstance(other, MutableSeq):
for c in other.data:
self.data.append(c)
else:
for c in other:
self.data.append(c)
def tostring(self):
return string.join(self.data, "")
def toseq(self):
return Seq(string.join(self.data, ""), self.alphabet)
# The transcribe, backward_transcribe, and translate functions are
# user-friendly versions of the corresponding functions in Bio.Transcribe
# and Bio.Translate. The functions work both on Seq objects, and on strings.
def transcribe(dna):
if isinstance(dna, Seq):
rna = dna.data.replace('T','U').replace('t','u')
if dna.alphabet==IUPAC.unambiguous_dna:
alphabet = IUPAC.unambiguous_rna
elif dna.alphabet==IUPAC.ambiguous_dna:
alphabet = IUPAC.ambiguous_rna
else:
alphabet = Alphabet.generic_rna
return Seq(rna, alphabet)
else:
rna = dna.replace('T','U').replace('t','u')
return rna
def back_transcribe(rna):
if isinstance(rna, Seq):
dna = rna.data.replace('U','T').replace('u','t')
if rna.alphabet==IUPAC.unambiguous_rna:
alphabet = IUPAC.unambiguous_dna
elif rna.alphabet==IUPAC.ambiguous_rna:
alphabet = IUPAC.ambiguous_dna
else:
alphabet = Alphabet.generic_dna
return Seq(dna, alphabet)
else:
dna = rna.replace('U','T').replace('u','t')
return dna
def translate(sequence, table = "Standard", stop_symbol = "*"):
try:
id = int(table)
except:
id = None
if isinstance(sequence, Seq):
if sequence.alphabet==IUPAC.unambiguous_dna:
if id==None:
table = CodonTable.unambiguous_dna_by_name[table]
else:
table = CodonTable.unambiguous_dna_by_id[id]
elif sequence.alphabet==IUPAC.ambiguous_dna:
if id==None:
table = CodonTable.ambiguous_dna_by_name[table]
else:
table = CodonTable.ambiguous_dna_by_id[id]
elif sequence.alphabet==IUPAC.unambiguous_rna:
if id==None:
table = CodonTable.unambiguous_rna_by_name[table]
else:
table = CodonTable.unambiguous_rna_by_id[id]
elif sequence.alphabet==IUPAC.ambiguous_rna:
if id==None:
table = CodonTable.ambiguous_rna_by_name[table]
else:
table = CodonTable.ambiguous_rna_by_id[id]
else:
if id==None:
table = CodonTable.generic_by_name[table]
else:
table = CodonTable.generic_by_id[id]
sequence = sequence.data.upper()
n = len(sequence)
get = table.forward_table.get
protein = [get(sequence[i:i+3], stop_symbol) for i in xrange(0,n-n%3,3)]
protein = "".join(protein)
alphabet = Alphabet.HasStopCodon(table.protein_alphabet)
return Seq(protein, alphabet)
else:
if id==None:
table = CodonTable.generic_by_name[table]
else:
table = CodonTable.generic_by_id[id]
get = table.forward_table.get
sequence = sequence.upper()
n = len(sequence)
protein = [get(sequence[i:i+3], stop_symbol) for i in xrange(0,n-n%3,3)]
protein = "".join(protein)
return protein
def reverse_complement(sequence):
"""Returns the reverse complement sequence. New string object.
"""
if 'U' in sequence:
ttable = string.maketrans("ACGUacgu","UGCAugca")
else:
ttable = string.maketrans("ACGTacgt","TGCAtgca")
sequence = sequence[-1::-1].translate(ttable)
return sequence
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