def back_transcribe(self):
"""Returns the DNA sequence from an RNA sequence. New Seq object.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG", \
IUPAC.unambiguous_rna)
>>> messenger_rna
Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA())
>>> messenger_rna.back_transcribe()
Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA())
Trying to back-transcribe a protein or DNA sequence raises an
exception.
>>> my_protein = Seq("MAIVMGR", IUPAC.protein)
>>> my_protein.back_transcribe()
Traceback (most recent call last):
...
ValueError: Proteins cannot be back transcribed!
"""
if isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.ProteinAlphabet):
raise ValueError("Proteins cannot be back transcribed!")
if isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.DNAAlphabet):
raise ValueError("DNA cannot be back transcribed!")
if self.alphabet == IUPAC.unambiguous_rna:
alphabet = IUPAC.unambiguous_dna
elif self.alphabet == IUPAC.ambiguous_rna:
alphabet = IUPAC.ambiguous_dna
else:
alphabet = Alphabet.generic_dna
return Seq(str(self).replace("U", "T").replace("u", "t"), alphabet)
def back_transcribe(self):
"""Returns the DNA sequence from an RNA sequence. New Seq object.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG", \
IUPAC.unambiguous_rna)
>>> messenger_rna
Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA())
>>> messenger_rna.back_transcribe()
Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA())
Trying to back-transcribe a protein or DNA sequence raises an
exception.
>>> my_protein = Seq("MAIVMGR", IUPAC.protein)
>>> my_protein.back_transcribe()
Traceback (most recent call last):
...
ValueError: Proteins cannot be back transcribed!
"""
if isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.ProteinAlphabet) :
raise ValueError("Proteins cannot be back transcribed!")
if isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.DNAAlphabet) :
raise ValueError("DNA cannot be back transcribed!")
if self.alphabet==IUPAC.unambiguous_rna:
alphabet = IUPAC.unambiguous_dna
elif self.alphabet==IUPAC.ambiguous_rna:
alphabet = IUPAC.ambiguous_dna
else:
alphabet = Alphabet.generic_dna
return Seq(str(self).replace("U", "T").replace("u", "t"), alphabet)
def complement(self):
"""Returns the complement sequence. New Seq object.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> my_dna = Seq("CCCCCGATAG", IUPAC.unambiguous_dna)
>>> my_dna
Seq('CCCCCGATAG', IUPACUnambiguousDNA())
>>> my_dna.complement()
Seq('GGGGGCTATC', IUPACUnambiguousDNA())
Trying to complement a protein sequence raises an exception.
>>> my_protein = Seq("MAIVMGR", IUPAC.protein)
>>> my_protein.complement()
Traceback (most recent call last):
...
ValueError: Proteins do not have complements!
"""
if isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.ProteinAlphabet):
raise ValueError("Proteins do not have complements!")
if isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.DNAAlphabet):
d = ambiguous_dna_complement
elif isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.RNAAlphabet):
d = ambiguous_rna_complement
elif 'U' in self._data and 'T' in self._data:
#TODO - Handle this cleanly?
raise ValueError("Mixed RNA/DNA found")
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 = str(self).translate(ttable)
return Seq(s, self.alphabet)
def complement(self):
"""Returns the complement sequence. New Seq object.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> my_dna = Seq("CCCCCGATAG", IUPAC.unambiguous_dna)
>>> my_dna
Seq('CCCCCGATAG', IUPACUnambiguousDNA())
>>> my_dna.complement()
Seq('GGGGGCTATC', IUPACUnambiguousDNA())
Trying to complement a protein sequence raises an exception.
>>> my_protein = Seq("MAIVMGR", IUPAC.protein)
>>> my_protein.complement()
Traceback (most recent call last):
...
ValueError: Proteins do not have complements!
"""
if isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.ProteinAlphabet) :
raise ValueError("Proteins do not have complements!")
if isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.DNAAlphabet) :
d = ambiguous_dna_complement
elif isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.RNAAlphabet) :
d = ambiguous_rna_complement
elif 'U' in self._data and 'T' in self._data:
#TODO - Handle this cleanly?
raise ValueError("Mixed RNA/DNA found")
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 = str(self).translate(ttable)
return Seq(s, self.alphabet)
def complement(self):
"""Modify the mutable sequence to take on its complement.
Trying to complement a protein sequence raises an exception.
No return value"""
if isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.ProteinAlphabet):
raise ValueError("Proteins do not have complements!")
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 and 'T' in self.data:
#TODO - Handle this cleanly?
raise ValueError("Mixed RNA/DNA found")
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 complement(self):
"""Modify the mutable sequence to take on its complement.
Trying to complement a protein sequence raises an exception.
No return value"""
if isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.ProteinAlphabet) :
raise ValueError("Proteins do not have complements!")
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 and 'T' in self.data :
#TODO - Handle this cleanly?
raise ValueError("Mixed RNA/DNA found")
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 translate(self, table="Standard", stop_symbol="*", to_stop=False):
"""Turns a nucleotide sequence into a protein sequence. New Seq object.
Trying to back-transcribe a protein sequence raises an exception.
This method will translate DNA or RNA sequences.
Trying to translate a protein sequence raises an exception.
table - Which codon table to use? This can be either a name
(string) or an NCBI identifier (integer). This defaults
to the "Standard" table.
stop_symbol - Single character string, what to use for terminators.
This defaults to the asterisk, "*".
to_stop - Boolean, defaults to False meaning do a full translation
continuing on past any stop codons (translated as the
specified stop_symbol). If True, translation is terminated
at the first in frame stop codon (and the stop_symbol is
not appended to the returned protein sequence).
e.g. Using the standard table,
>>> coding_dna = Seq("GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG")
>>> coding_dna.translate()
Seq('VAIVMGR*KGAR*', HasStopCodon(ExtendedIUPACProtein(), '*'))
>>> coding_dna.translate(stop_symbol="@")
Seq('VAIVMGR@KGAR@', HasStopCodon(ExtendedIUPACProtein(), '@'))
>>> coding_dna.translate(to_stop=True)
Seq('VAIVMGR', ExtendedIUPACProtein())
Now using NCBI table 2, where TGA is not a stop codon:
>>> coding_dna.translate(table=2)
Seq('VAIVMGRWKGAR*', HasStopCodon(ExtendedIUPACProtein(), '*'))
>>> coding_dna.translate(table=2, to_stop=True)
Seq('VAIVMGRWKGAR', ExtendedIUPACProtein())
If the sequence has no in-frame stop codon, then the to_stop argument
has no effect:
>>> coding_dna2 = Seq("TTGGCCATTGTAATGGGCCGC")
>>> coding_dna2.translate()
Seq('LAIVMGR', ExtendedIUPACProtein())
>>> coding_dna2.translate(to_stop=True)
Seq('LAIVMGR', ExtendedIUPACProtein())
NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid
or a stop codon. These are translated as "X". Any invalid codon
(e.g. "TA?" or "T-A") will throw a TranslationError.
NOTE - Does NOT support gapped sequences.
NOTE - This does NOT behave like the python string's translate
method. For that use str(my_seq).translate(...) instead.
"""
try:
table_id = int(table)
except ValueError:
table_id = None
if isinstance(table, str) and len(table) == 256:
raise ValueError("The Seq object translate method DOES NOT take " \
+ "a 256 character string mapping table like " \
+ "the python string object's translate method. " \
+ "Use str(my_seq).translate(...) instead.")
if isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.ProteinAlphabet):
raise ValueError("Proteins cannot be translated!")
if self.alphabet == IUPAC.unambiguous_dna:
if table_id is None:
codon_table = CodonTable.unambiguous_dna_by_name[table]
else:
codon_table = CodonTable.unambiguous_dna_by_id[table_id]
elif self.alphabet == IUPAC.ambiguous_dna:
if table_id is None:
codon_table = CodonTable.ambiguous_dna_by_name[table]
else:
codon_table = CodonTable.ambiguous_dna_by_id[table_id]
elif self.alphabet == IUPAC.unambiguous_rna:
if table_id is None:
codon_table = CodonTable.unambiguous_rna_by_name[table]
else:
codon_table = CodonTable.unambiguous_rna_by_id[table_id]
elif self.alphabet == IUPAC.ambiguous_rna:
if table_id is None:
codon_table = CodonTable.ambiguous_rna_by_name[table]
else:
codon_table = CodonTable.ambiguous_rna_by_id[table_id]
else:
if table_id is None:
codon_table = CodonTable.ambiguous_generic_by_name[table]
else:
codon_table = CodonTable.ambiguous_generic_by_id[table_id]
protein = _translate_str(str(self), codon_table, stop_symbol, to_stop)
if stop_symbol in protein:
alphabet = Alphabet.HasStopCodon(codon_table.protein_alphabet,
stop_symbol=stop_symbol)
else:
alphabet = codon_table.protein_alphabet
return Seq(protein, alphabet)
def translate(self, table="Standard", stop_symbol="*", to_stop=False):
"""Turns a nucleotide sequence into a protein sequence. New Seq object.
Trying to back-transcribe a protein sequence raises an exception.
This method will translate DNA or RNA sequences.
Trying to translate a protein sequence raises an exception.
table - Which codon table to use? This can be either a name
(string) or an NCBI identifier (integer). This defaults
to the "Standard" table.
stop_symbol - Single character string, what to use for terminators.
This defaults to the asterisk, "*".
to_stop - Boolean, defaults to False meaning do a full translation
continuing on past any stop codons (translated as the
specified stop_symbol). If True, translation is terminated
at the first in frame stop codon (and the stop_symbol is
not appended to the returned protein sequence).
e.g. Using the standard table,
>>> coding_dna = Seq("GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG")
>>> coding_dna.translate()
Seq('VAIVMGR*KGAR*', HasStopCodon(ExtendedIUPACProtein(), '*'))
>>> coding_dna.translate(stop_symbol="@")
Seq('VAIVMGR@KGAR@', HasStopCodon(ExtendedIUPACProtein(), '@'))
>>> coding_dna.translate(to_stop=True)
Seq('VAIVMGR', ExtendedIUPACProtein())
Now using NCBI table 2, where TGA is not a stop codon:
>>> coding_dna.translate(table=2)
Seq('VAIVMGRWKGAR*', HasStopCodon(ExtendedIUPACProtein(), '*'))
>>> coding_dna.translate(table=2, to_stop=True)
Seq('VAIVMGRWKGAR', ExtendedIUPACProtein())
If the sequence has no in-frame stop codon, then the to_stop argument
has no effect:
>>> coding_dna2 = Seq("TTGGCCATTGTAATGGGCCGC")
>>> coding_dna2.translate()
Seq('LAIVMGR', ExtendedIUPACProtein())
>>> coding_dna2.translate(to_stop=True)
Seq('LAIVMGR', ExtendedIUPACProtein())
NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid
or a stop codon. These are translated as "X". Any invalid codon
(e.g. "TA?" or "T-A") will throw a TranslationError.
NOTE - Does NOT support gapped sequences.
NOTE - This does NOT behave like the python string's translate
method. For that use str(my_seq).translate(...) instead.
"""
try:
table_id = int(table)
except ValueError:
table_id = None
if isinstance(table, str) and len(table)==256 :
raise ValueError("The Seq object translate method DOES NOT take " \
+ "a 256 character string mapping table like " \
+ "the python string object's translate method. " \
+ "Use str(my_seq).translate(...) instead.")
if isinstance(Alphabet._get_base_alphabet(self.alphabet),
Alphabet.ProteinAlphabet) :
raise ValueError("Proteins cannot be translated!")
if self.alphabet==IUPAC.unambiguous_dna:
if table_id is None:
codon_table = CodonTable.unambiguous_dna_by_name[table]
else:
codon_table = CodonTable.unambiguous_dna_by_id[table_id]
elif self.alphabet==IUPAC.ambiguous_dna:
if table_id is None:
codon_table = CodonTable.ambiguous_dna_by_name[table]
else:
codon_table = CodonTable.ambiguous_dna_by_id[table_id]
elif self.alphabet==IUPAC.unambiguous_rna:
if table_id is None:
codon_table = CodonTable.unambiguous_rna_by_name[table]
else:
codon_table = CodonTable.unambiguous_rna_by_id[table_id]
elif self.alphabet==IUPAC.ambiguous_rna:
if table_id is None:
codon_table = CodonTable.ambiguous_rna_by_name[table]
else:
codon_table = CodonTable.ambiguous_rna_by_id[table_id]
else:
if table_id is None:
codon_table = CodonTable.ambiguous_generic_by_name[table]
else:
codon_table = CodonTable.ambiguous_generic_by_id[table_id]
protein = _translate_str(str(self), codon_table, stop_symbol, to_stop)
if stop_symbol in protein :
alphabet = Alphabet.HasStopCodon(codon_table.protein_alphabet,
stop_symbol = stop_symbol)
else :
alphabet = codon_table.protein_alphabet
return Seq(protein, alphabet)
