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PlantAI-dev/tools/interproscan-5.78-109.0/bin/panther/Bio/Seq.py
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# Copyright 2000 Andrew Dalke.
# Copyright 2000-2002 Brad Chapman.
# Copyright 2004-2005, 2010 by M de Hoon.
# Copyright 2007-2018 by Peter Cock.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Provide objects to represent biological sequences with alphabets.
See also the Seq_ wiki and the chapter in our tutorial:
- `HTML Tutorial`_
- `PDF Tutorial`_
.. _Seq: http://biopython.org/wiki/Seq
.. _`HTML Tutorial`: http://biopython.org/DIST/docs/tutorial/Tutorial.html
.. _`PDF Tutorial`: http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
"""
from __future__ import print_function
import string # for maketrans only
import array
import sys
import warnings
import collections
try:
# Python 3
from collections.abc import Iterable as _Iterable
except ImportError:
# Python 2.7
from collections import Iterable as _Iterable
from Bio._py3k import range
from Bio._py3k import basestring
from Bio import BiopythonWarning
from Bio import Alphabet
from Bio.Alphabet import IUPAC
from Bio.Data.IUPACData import ambiguous_dna_complement, ambiguous_rna_complement
from Bio.Data.IUPACData import ambiguous_dna_letters as _ambiguous_dna_letters
from Bio.Data.IUPACData import ambiguous_rna_letters as _ambiguous_rna_letters
from Bio.Data import CodonTable
def _maketrans(complement_mapping):
"""Make a python string translation table (PRIVATE).
Arguments:
- complement_mapping - a dictionary such as ambiguous_dna_complement
and ambiguous_rna_complement from Data.IUPACData.
Returns a translation table (a string of length 256) for use with the
python string's translate method to use in a (reverse) complement.
Compatible with lower case and upper case sequences.
For internal use only.
"""
before = "".join(complement_mapping.keys())
after = "".join(complement_mapping.values())
before += before.lower()
after += after.lower()
if sys.version_info[0] == 3:
return str.maketrans(before, after)
else:
return string.maketrans(before, after)
_dna_complement_table = _maketrans(ambiguous_dna_complement)
_rna_complement_table = _maketrans(ambiguous_rna_complement)
class Seq(object):
"""Read-only sequence object (essentially a string with an alphabet).
Like normal python strings, our basic sequence object is immutable.
This prevents you from doing my_seq[5] = "A" for example, but does allow
Seq objects to be used as dictionary keys.
The Seq object provides a number of string like methods (such as count,
find, split and strip), which are alphabet aware where appropriate.
In addition to the string like sequence, the Seq object has an alphabet
property. This is an instance of an Alphabet class from Bio.Alphabet,
for example generic DNA, or IUPAC DNA. This describes the type of molecule
(e.g. RNA, DNA, protein) and may also indicate the expected symbols
(letters).
The Seq object also provides some biological methods, such as complement,
reverse_complement, transcribe, back_transcribe and translate (which are
not applicable to sequences with a protein alphabet).
"""
def __init__(self, data, alphabet=Alphabet.generic_alphabet):
"""Create a Seq object.
Arguments:
- seq - Sequence, required (string)
- alphabet - Optional argument, an Alphabet object from
Bio.Alphabet
You will typically use Bio.SeqIO to read in sequences from files as
SeqRecord objects, whose sequence will be exposed as a Seq object via
the seq property.
However, will often want to create your own Seq objects directly:
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> my_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
... IUPAC.protein)
>>> my_seq
Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())
>>> print(my_seq)
MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
>>> my_seq.alphabet
IUPACProtein()
"""
# Enforce string storage
if not isinstance(data, basestring):
raise TypeError(
"The sequence data given to a Seq object should "
"be a string (not another Seq object etc)"
)
self._data = data
self.alphabet = alphabet # Seq API requirement
def __repr__(self):
"""Return (truncated) representation of the sequence for debugging."""
if self.alphabet is Alphabet.generic_alphabet:
# Default used, we can omit it and simplify the representation
a = ""
else:
a = ", %r" % self.alphabet
if len(self) > 60:
# Shows the last three letters as it is often useful to see if
# there is a stop codon at the end of a sequence.
# Note total length is 54+3+3=60
return "{0}('{1}...{2}'{3!s})".format(
self.__class__.__name__, str(self)[:54], str(self)[-3:], a
)
else:
return "{0}({1!r}{2!s})".format(self.__class__.__name__, self._data, a)
def __str__(self):
"""Return the full sequence as a python string, use str(my_seq).
Note that Biopython 1.44 and earlier would give a truncated
version of repr(my_seq) for str(my_seq). If you are writing code
which need to be backwards compatible with really old Biopython,
you should continue to use my_seq.tostring() as follows::
try:
# The old way, removed in Biopython 1.73
as_string = seq_obj.tostring()
except AttributeError:
# The new way, needs Biopython 1.45 or later.
# Don't use this on Biopython 1.44 or older as truncates
as_string = str(seq_obj)
"""
return self._data
def __hash__(self):
"""Hash for comparison.
See the __cmp__ documentation - this has changed from past
versions of Biopython!
"""
# TODO - remove this warning in a future release
warnings.warn(
"Biopython Seq objects now use string comparison. "
"Older versions of Biopython used object comparison. "
"During this transition, please use hash(id(my_seq)) "
"or my_dict[id(my_seq)] if you want the old behaviour, "
"or use hash(str(my_seq)) or my_dict[str(my_seq)] for "
"the new string hashing behaviour.",
BiopythonWarning,
)
return hash(str(self))
def __eq__(self, other):
"""Compare the sequence to another sequence or a string (README).
Historically comparing Seq objects has done Python object comparison.
After considerable discussion (keeping in mind constraints of the
Python language, hashes and dictionary support), Biopython now uses
simple string comparison (with a warning about the change).
Note that incompatible alphabets (e.g. DNA to RNA) will trigger a
warning.
During this transition period, please just do explicit comparisons:
>>> from Bio.Seq import Seq
>>> seq1 = Seq("ACGT")
>>> seq2 = Seq("ACGT")
>>> id(seq1) == id(seq2)
False
>>> str(seq1) == str(seq2)
True
The new behaviour is to use string-like equality:
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_dna
>>> seq1 == seq2
True
>>> seq1 == "ACGT"
True
>>> seq1 == Seq("ACGT", generic_dna)
True
"""
if hasattr(other, "alphabet"):
# other could be a Seq or a MutableSeq
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
warnings.warn(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
),
BiopythonWarning,
)
return str(self) == str(other)
def __ne__(self, other):
"""Implement the not-equal operand."""
# Require this method for Python 2 but not needed on Python 3
return not self == other
def __lt__(self, other):
"""Implement the less-than operand."""
if hasattr(other, "alphabet"):
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
warnings.warn(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
),
BiopythonWarning,
)
if isinstance(other, (str, Seq, MutableSeq, UnknownSeq)):
return str(self) < str(other)
raise TypeError(
"'<' not supported between instances of '{}' and '{}'".format(
type(self).__name__, type(other).__name__
)
)
def __le__(self, other):
"""Implement the less-than or equal operand."""
if hasattr(other, "alphabet"):
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
warnings.warn(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
),
BiopythonWarning,
)
if isinstance(other, (str, Seq, MutableSeq, UnknownSeq)):
return str(self) <= str(other)
raise TypeError(
"'<=' not supported between instances of '{}' and '{}'".format(
type(self).__name__, type(other).__name__
)
)
def __gt__(self, other):
"""Implement the greater-than operand."""
if hasattr(other, "alphabet"):
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
warnings.warn(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
),
BiopythonWarning,
)
if isinstance(other, (str, Seq, MutableSeq, UnknownSeq)):
return str(self) > str(other)
raise TypeError(
"'>' not supported between instances of '{}' and '{}'".format(
type(self).__name__, type(other).__name__
)
)
def __ge__(self, other):
"""Implement the greater-than or equal operand."""
if hasattr(other, "alphabet"):
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
warnings.warn(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
),
BiopythonWarning,
)
if isinstance(other, (str, Seq, MutableSeq, UnknownSeq)):
return str(self) >= str(other)
raise TypeError(
"'>=' not supported between instances of '{}' and '{}'".format(
type(self).__name__, type(other).__name__
)
)
def __len__(self):
"""Return the length of the sequence, use len(my_seq)."""
return len(self._data) # Seq API requirement
def __getitem__(self, index): # Seq API requirement
"""Return a subsequence of single letter, use my_seq[index].
>>> my_seq = Seq('ACTCGACGTCG')
>>> my_seq[5]
'A'
"""
# Note since Python 2.0, __getslice__ is deprecated
# and __getitem__ is used instead.
# See http://docs.python.org/ref/sequence-methods.html
if isinstance(index, int):
# Return a single letter as a string
return self._data[index]
else:
# Return the (sub)sequence as another Seq object
return Seq(self._data[index], self.alphabet)
def __add__(self, other):
"""Add another sequence or string to this sequence.
If adding a string to a Seq, the alphabet is preserved:
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_protein
>>> Seq("MELKI", generic_protein) + "LV"
Seq('MELKILV', ProteinAlphabet())
When adding two Seq (like) objects, the alphabets are important.
Consider this example:
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet.IUPAC import unambiguous_dna, ambiguous_dna
>>> unamb_dna_seq = Seq("ACGT", unambiguous_dna)
>>> ambig_dna_seq = Seq("ACRGT", ambiguous_dna)
>>> unamb_dna_seq
Seq('ACGT', IUPACUnambiguousDNA())
>>> ambig_dna_seq
Seq('ACRGT', IUPACAmbiguousDNA())
If we add the ambiguous and unambiguous IUPAC DNA alphabets, we get
the more general ambiguous IUPAC DNA alphabet:
>>> unamb_dna_seq + ambig_dna_seq
Seq('ACGTACRGT', IUPACAmbiguousDNA())
However, if the default generic alphabet is included, the result is
a generic alphabet:
>>> Seq("") + ambig_dna_seq
Seq('ACRGT')
You can't add RNA and DNA sequences:
>>> from Bio.Alphabet import generic_dna, generic_rna
>>> Seq("ACGT", generic_dna) + Seq("ACGU", generic_rna)
Traceback (most recent call last):
...
TypeError: Incompatible alphabets DNAAlphabet() and RNAAlphabet()
You can't add nucleotide and protein sequences:
>>> from Bio.Alphabet import generic_dna, generic_protein
>>> Seq("ACGT", generic_dna) + Seq("MELKI", generic_protein)
Traceback (most recent call last):
...
TypeError: Incompatible alphabets DNAAlphabet() and ProteinAlphabet()
"""
if hasattr(other, "alphabet"):
# other should be a Seq or a MutableSeq
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
raise TypeError(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
)
)
# They should be the same sequence type (or one of them is generic)
a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet])
return self.__class__(str(self) + str(other), a)
elif isinstance(other, basestring):
# other is a plain string - use the current alphabet
return self.__class__(str(self) + other, self.alphabet)
from Bio.SeqRecord import SeqRecord # Lazy to avoid circular imports
if isinstance(other, SeqRecord):
# Get the SeqRecord's __radd__ to handle this
return NotImplemented
else:
raise TypeError
def __radd__(self, other):
"""Add a sequence on the left.
If adding a string to a Seq, the alphabet is preserved:
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_protein
>>> "LV" + Seq("MELKI", generic_protein)
Seq('LVMELKI', ProteinAlphabet())
Adding two Seq (like) objects is handled via the __add__ method.
"""
if hasattr(other, "alphabet"):
# other should be a Seq or a MutableSeq
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
raise TypeError(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
)
)
# They should be the same sequence type (or one of them is generic)
a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet])
return self.__class__(str(other) + str(self), a)
elif isinstance(other, basestring):
# other is a plain string - use the current alphabet
return self.__class__(other + str(self), self.alphabet)
else:
raise TypeError
def __mul__(self, other):
"""Multiply Seq by integer.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_dna
>>> Seq('ATG') * 2
Seq('ATGATG')
>>> Seq('ATG', generic_dna) * 2
Seq('ATGATG', DNAAlphabet())
"""
if not isinstance(other, int):
raise TypeError(
"can't multiply {} by non-int type".format(self.__class__.__name__)
)
return self.__class__(str(self) * other, self.alphabet)
def __rmul__(self, other):
"""Multiply integer by Seq.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_dna
>>> 2 * Seq('ATG')
Seq('ATGATG')
>>> 2 * Seq('ATG', generic_dna)
Seq('ATGATG', DNAAlphabet())
"""
if not isinstance(other, int):
raise TypeError(
"can't multiply {} by non-int type".format(self.__class__.__name__)
)
return self.__class__(str(self) * other, self.alphabet)
def __imul__(self, other):
"""Multiply Seq in-place.
Note although Seq is immutable, the in-place method is
included to match the behaviour for regular Python strings.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_dna
>>> seq = Seq('ATG', generic_dna)
>>> seq *= 2
>>> seq
Seq('ATGATG', DNAAlphabet())
"""
if not isinstance(other, int):
raise TypeError(
"can't multiply {} by non-int type".format(self.__class__.__name__)
)
return self.__class__(str(self) * other, self.alphabet)
def tomutable(self): # Needed? Or use a function?
"""Return the full sequence as a MutableSeq object.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> my_seq = Seq("MKQHKAMIVALIVICITAVVAAL",
... IUPAC.protein)
>>> my_seq
Seq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
>>> my_seq.tomutable()
MutableSeq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
Note that the alphabet is preserved.
"""
return MutableSeq(str(self), self.alphabet)
def _get_seq_str_and_check_alphabet(self, other_sequence):
"""Convert string/Seq/MutableSeq to string, checking alphabet (PRIVATE).
For a string argument, returns the string.
For a Seq or MutableSeq, it checks the alphabet is compatible
(raising an exception if it isn't), and then returns a string.
"""
try:
other_alpha = other_sequence.alphabet
except AttributeError:
# Assume other_sequence is a string
return other_sequence
# Other should be a Seq or a MutableSeq
if not Alphabet._check_type_compatible([self.alphabet, other_alpha]):
raise TypeError(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other_alpha
)
)
# Return as a string
return str(other_sequence)
def count(self, sub, start=0, end=sys.maxsize):
"""Return a non-overlapping count, like that of a python string.
This behaves like the python string method of the same name,
which does a non-overlapping count!
For an overlapping search use the newer count_overlap() method.
Returns an integer, the number of occurrences of substring
argument sub in the (sub)sequence given by [start:end].
Optional arguments start and end are interpreted as in slice
notation.
Arguments:
- sub - a string or another Seq object to look for
- start - optional integer, slice start
- end - optional integer, slice end
e.g.
>>> from Bio.Seq import Seq
>>> my_seq = Seq("AAAATGA")
>>> print(my_seq.count("A"))
5
>>> print(my_seq.count("ATG"))
1
>>> print(my_seq.count(Seq("AT")))
1
>>> print(my_seq.count("AT", 2, -1))
1
HOWEVER, please note because python strings and Seq objects (and
MutableSeq objects) do a non-overlapping search, this may not give
the answer you expect:
>>> "AAAA".count("AA")
2
>>> print(Seq("AAAA").count("AA"))
2
An overlapping search, as implemented in .count_overlap(),
would give the answer as three!
"""
# If it has one, check the alphabet:
sub_str = self._get_seq_str_and_check_alphabet(sub)
return str(self).count(sub_str, start, end)
def count_overlap(self, sub, start=0, end=sys.maxsize):
"""Return an overlapping count.
For a non-overlapping search use the count() method.
Returns an integer, the number of occurrences of substring
argument sub in the (sub)sequence given by [start:end].
Optional arguments start and end are interpreted as in slice
notation.
Arguments:
- sub - a string or another Seq object to look for
- start - optional integer, slice start
- end - optional integer, slice end
e.g.
>>> from Bio.Seq import Seq
>>> print(Seq("AAAA").count_overlap("AA"))
3
>>> print(Seq("ATATATATA").count_overlap("ATA"))
4
>>> print(Seq("ATATATATA").count_overlap("ATA", 3, -1))
1
Where substrings do not overlap, should behave the same as
the count() method:
>>> from Bio.Seq import Seq
>>> my_seq = Seq("AAAATGA")
>>> print(my_seq.count_overlap("A"))
5
>>> my_seq.count_overlap("A") == my_seq.count("A")
True
>>> print(my_seq.count_overlap("ATG"))
1
>>> my_seq.count_overlap("ATG") == my_seq.count("ATG")
True
>>> print(my_seq.count_overlap(Seq("AT")))
1
>>> my_seq.count_overlap(Seq("AT")) == my_seq.count(Seq("AT"))
True
>>> print(my_seq.count_overlap("AT", 2, -1))
1
>>> my_seq.count_overlap("AT", 2, -1) == my_seq.count("AT", 2, -1)
True
HOWEVER, do not use this method for such cases because the
count() method is much for efficient.
"""
sub_str = self._get_seq_str_and_check_alphabet(sub)
self_str = str(self)
overlap_count = 0
while True:
start = self_str.find(sub_str, start, end) + 1
if start != 0:
overlap_count += 1
else:
return overlap_count
def __contains__(self, char):
"""Implement the 'in' keyword, like a python string.
e.g.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_dna, generic_rna, generic_protein
>>> my_dna = Seq("ATATGAAATTTGAAAA", generic_dna)
>>> "AAA" in my_dna
True
>>> Seq("AAA") in my_dna
True
>>> Seq("AAA", generic_dna) in my_dna
True
Like other Seq methods, this will raise a type error if another Seq
(or Seq like) object with an incompatible alphabet is used:
>>> Seq("AAA", generic_rna) in my_dna
Traceback (most recent call last):
...
TypeError: Incompatible alphabets DNAAlphabet() and RNAAlphabet()
>>> Seq("AAA", generic_protein) in my_dna
Traceback (most recent call last):
...
TypeError: Incompatible alphabets DNAAlphabet() and ProteinAlphabet()
"""
# If it has one, check the alphabet:
sub_str = self._get_seq_str_and_check_alphabet(char)
return sub_str in str(self)
def find(self, sub, start=0, end=sys.maxsize):
"""Find method, like that of a python string.
This behaves like the python string method of the same name.
Returns an integer, the index of the first occurrence of substring
argument sub in the (sub)sequence given by [start:end].
Arguments:
- sub - a string or another Seq object to look for
- start - optional integer, slice start
- end - optional integer, slice end
Returns -1 if the subsequence is NOT found.
e.g. Locating the first typical start codon, AUG, in an RNA sequence:
>>> from Bio.Seq import Seq
>>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
>>> my_rna.find("AUG")
3
"""
# If it has one, check the alphabet:
sub_str = self._get_seq_str_and_check_alphabet(sub)
return str(self).find(sub_str, start, end)
def rfind(self, sub, start=0, end=sys.maxsize):
"""Find from right method, like that of a python string.
This behaves like the python string method of the same name.
Returns an integer, the index of the last (right most) occurrence of
substring argument sub in the (sub)sequence given by [start:end].
Arguments:
- sub - a string or another Seq object to look for
- start - optional integer, slice start
- end - optional integer, slice end
Returns -1 if the subsequence is NOT found.
e.g. Locating the last typical start codon, AUG, in an RNA sequence:
>>> from Bio.Seq import Seq
>>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
>>> my_rna.rfind("AUG")
15
"""
# If it has one, check the alphabet:
sub_str = self._get_seq_str_and_check_alphabet(sub)
return str(self).rfind(sub_str, start, end)
def index(self, sub, start=0, end=sys.maxsize):
"""Like find() but raise ValueError when the substring is not found.
>>> from Bio.Seq import Seq
>>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
>>> my_rna.find("T")
-1
>>> my_rna.index("T")
Traceback (most recent call last):
...
ValueError: substring not found...
"""
# If it has one, check the alphabet:
sub_str = self._get_seq_str_and_check_alphabet(sub)
return str(self).index(sub_str, start, end)
def rindex(self, sub, start=0, end=sys.maxsize):
"""Like rfind() but raise ValueError when the substring is not found."""
# If it has one, check the alphabet:
sub_str = self._get_seq_str_and_check_alphabet(sub)
return str(self).rindex(sub_str, start, end)
def startswith(self, prefix, start=0, end=sys.maxsize):
"""Return True if the Seq starts with the given prefix, False otherwise.
This behaves like the python string method of the same name.
Return True if the sequence starts with the specified prefix
(a string or another Seq object), False otherwise.
With optional start, test sequence beginning at that position.
With optional end, stop comparing sequence at that position.
prefix can also be a tuple of strings to try. e.g.
>>> from Bio.Seq import Seq
>>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
>>> my_rna.startswith("GUC")
True
>>> my_rna.startswith("AUG")
False
>>> my_rna.startswith("AUG", 3)
True
>>> my_rna.startswith(("UCC", "UCA", "UCG"), 1)
True
"""
# If it has one, check the alphabet:
if isinstance(prefix, tuple):
prefix_strs = tuple(self._get_seq_str_and_check_alphabet(p) for p in prefix)
return str(self).startswith(prefix_strs, start, end)
else:
prefix_str = self._get_seq_str_and_check_alphabet(prefix)
return str(self).startswith(prefix_str, start, end)
def endswith(self, suffix, start=0, end=sys.maxsize):
"""Return True if the Seq ends with the given suffix, False otherwise.
This behaves like the python string method of the same name.
Return True if the sequence ends with the specified suffix
(a string or another Seq object), False otherwise.
With optional start, test sequence beginning at that position.
With optional end, stop comparing sequence at that position.
suffix can also be a tuple of strings to try. e.g.
>>> from Bio.Seq import Seq
>>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
>>> my_rna.endswith("UUG")
True
>>> my_rna.endswith("AUG")
False
>>> my_rna.endswith("AUG", 0, 18)
True
>>> my_rna.endswith(("UCC", "UCA", "UUG"))
True
"""
# If it has one, check the alphabet:
if isinstance(suffix, tuple):
suffix_strs = tuple(self._get_seq_str_and_check_alphabet(p) for p in suffix)
return str(self).endswith(suffix_strs, start, end)
else:
suffix_str = self._get_seq_str_and_check_alphabet(suffix)
return str(self).endswith(suffix_str, start, end)
def split(self, sep=None, maxsplit=-1):
"""Split method, like that of a python string.
This behaves like the python string method of the same name.
Return a list of the 'words' in the string (as Seq objects),
using sep as the delimiter string. If maxsplit is given, at
most maxsplit splits are done. If maxsplit is omitted, all
splits are made.
Following the python string method, sep will by default be any
white space (tabs, spaces, newlines) but this is unlikely to
apply to biological sequences.
e.g.
>>> from Bio.Seq import Seq
>>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
>>> my_aa = my_rna.translate()
>>> my_aa
Seq('VMAIVMGR*KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*'))
>>> for pep in my_aa.split("*"):
... pep
Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*'))
Seq('KGAR', HasStopCodon(ExtendedIUPACProtein(), '*'))
Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))
>>> for pep in my_aa.split("*", 1):
... pep
Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*'))
Seq('KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*'))
See also the rsplit method:
>>> for pep in my_aa.rsplit("*", 1):
... pep
Seq('VMAIVMGR*KGAR', HasStopCodon(ExtendedIUPACProtein(), '*'))
Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))
"""
# If it has one, check the alphabet:
sep_str = self._get_seq_str_and_check_alphabet(sep)
# TODO - If the sep is the defined stop symbol, or gap char,
# should we adjust the alphabet?
return [Seq(part, self.alphabet) for part in str(self).split(sep_str, maxsplit)]
def rsplit(self, sep=None, maxsplit=-1):
"""Do a right split method, like that of a python string.
This behaves like the python string method of the same name.
Return a list of the 'words' in the string (as Seq objects),
using sep as the delimiter string. If maxsplit is given, at
most maxsplit splits are done COUNTING FROM THE RIGHT.
If maxsplit is omitted, all splits are made.
Following the python string method, sep will by default be any
white space (tabs, spaces, newlines) but this is unlikely to
apply to biological sequences.
e.g. print(my_seq.rsplit("*",1))
See also the split method.
"""
# If it has one, check the alphabet:
sep_str = self._get_seq_str_and_check_alphabet(sep)
return [
Seq(part, self.alphabet) for part in str(self).rsplit(sep_str, maxsplit)
]
def strip(self, chars=None):
"""Return a new Seq object with leading and trailing ends stripped.
This behaves like the python string method of the same name.
Optional argument chars defines which characters to remove. If
omitted or None (default) then as for the python string method,
this defaults to removing any white space.
e.g. print(my_seq.strip("-"))
See also the lstrip and rstrip methods.
"""
# If it has one, check the alphabet:
strip_str = self._get_seq_str_and_check_alphabet(chars)
return Seq(str(self).strip(strip_str), self.alphabet)
def lstrip(self, chars=None):
"""Return a new Seq object with leading (left) end stripped.
This behaves like the python string method of the same name.
Optional argument chars defines which characters to remove. If
omitted or None (default) then as for the python string method,
this defaults to removing any white space.
e.g. print(my_seq.lstrip("-"))
See also the strip and rstrip methods.
"""
# If it has one, check the alphabet:
strip_str = self._get_seq_str_and_check_alphabet(chars)
return Seq(str(self).lstrip(strip_str), self.alphabet)
def rstrip(self, chars=None):
"""Return a new Seq object with trailing (right) end stripped.
This behaves like the python string method of the same name.
Optional argument chars defines which characters to remove. If
omitted or None (default) then as for the python string method,
this defaults to removing any white space.
e.g. Removing a nucleotide sequence's polyadenylation (poly-A tail):
>>> from Bio.Alphabet import IUPAC
>>> from Bio.Seq import Seq
>>> my_seq = Seq("CGGTACGCTTATGTCACGTAGAAAAAA", IUPAC.unambiguous_dna)
>>> my_seq
Seq('CGGTACGCTTATGTCACGTAGAAAAAA', IUPACUnambiguousDNA())
>>> my_seq.rstrip("A")
Seq('CGGTACGCTTATGTCACGTAG', IUPACUnambiguousDNA())
See also the strip and lstrip methods.
"""
# If it has one, check the alphabet:
strip_str = self._get_seq_str_and_check_alphabet(chars)
return Seq(str(self).rstrip(strip_str), self.alphabet)
def upper(self):
"""Return an upper case copy of the sequence.
>>> from Bio.Alphabet import HasStopCodon, generic_protein
>>> from Bio.Seq import Seq
>>> my_seq = Seq("VHLTPeeK*", HasStopCodon(generic_protein))
>>> my_seq
Seq('VHLTPeeK*', HasStopCodon(ProteinAlphabet(), '*'))
>>> my_seq.lower()
Seq('vhltpeek*', HasStopCodon(ProteinAlphabet(), '*'))
>>> my_seq.upper()
Seq('VHLTPEEK*', HasStopCodon(ProteinAlphabet(), '*'))
This will adjust the alphabet if required. See also the lower method.
"""
return Seq(str(self).upper(), self.alphabet._upper())
def lower(self):
"""Return a lower case copy of the sequence.
This will adjust the alphabet if required. Note that the IUPAC
alphabets are upper case only, and thus a generic alphabet must be
substituted.
>>> from Bio.Alphabet import Gapped, generic_dna
>>> from Bio.Alphabet import IUPAC
>>> from Bio.Seq import Seq
>>> my_seq = Seq("CGGTACGCTTATGTCACGTAG*AAAAAA",
... Gapped(IUPAC.unambiguous_dna, "*"))
>>> my_seq
Seq('CGGTACGCTTATGTCACGTAG*AAAAAA', Gapped(IUPACUnambiguousDNA(), '*'))
>>> my_seq.lower()
Seq('cggtacgcttatgtcacgtag*aaaaaa', Gapped(DNAAlphabet(), '*'))
See also the upper method.
"""
return Seq(str(self).lower(), self.alphabet._lower())
def encode(self, encoding="utf-8", errors="strict"):
"""Return an encoded version of the sequence as a bytes object.
The Seq object aims to match the interfact of a Python string.
(This means on Python 3 it acts like a unicode string.)
This is essentially to save you doing str(my_seq).encode() when
you need a bytes string, for example for computing a hash:
>>> from Bio.Seq import Seq
>>> Seq("ACGT").encode("ascii")
b'ACGT'
"""
return str(self).encode(encoding, errors)
def complement(self):
"""Return the complement sequence by creating a 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())
You can of course used mixed case sequences,
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_dna
>>> my_dna = Seq("CCCCCgatA-GD", generic_dna)
>>> my_dna
Seq('CCCCCgatA-GD', DNAAlphabet())
>>> my_dna.complement()
Seq('GGGGGctaT-CH', DNAAlphabet())
Note in the above example, ambiguous character D denotes
G, A or T so its complement is H (for C, T or A).
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!
"""
base = Alphabet._get_base_alphabet(self.alphabet)
if isinstance(base, Alphabet.ProteinAlphabet):
raise ValueError("Proteins do not have complements!")
if isinstance(base, Alphabet.DNAAlphabet):
ttable = _dna_complement_table
elif isinstance(base, Alphabet.RNAAlphabet):
ttable = _rna_complement_table
elif ("U" in self._data or "u" in self._data) and (
"T" in self._data or "t" in self._data
):
# TODO - Handle this cleanly?
raise ValueError("Mixed RNA/DNA found")
elif "U" in self._data or "u" in self._data:
ttable = _rna_complement_table
else:
ttable = _dna_complement_table
# Much faster on really long sequences than the previous loop based
# one. Thanks to Michael Palmer, University of Waterloo.
return Seq(str(self).translate(ttable), self.alphabet)
def reverse_complement(self):
"""Return the reverse complement sequence by creating a new Seq object.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> my_dna = Seq("CCCCCGATAGNR", IUPAC.ambiguous_dna)
>>> my_dna
Seq('CCCCCGATAGNR', IUPACAmbiguousDNA())
>>> my_dna.reverse_complement()
Seq('YNCTATCGGGGG', IUPACAmbiguousDNA())
Note in the above example, since R = G or A, its complement
is Y (which denotes C or T).
You can of course used mixed case sequences,
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_dna
>>> my_dna = Seq("CCCCCgatA-G", generic_dna)
>>> my_dna
Seq('CCCCCgatA-G', DNAAlphabet())
>>> my_dna.reverse_complement()
Seq('C-TatcGGGGG', DNAAlphabet())
Trying to complement a protein sequence raises an exception:
>>> my_protein = Seq("MAIVMGR", IUPAC.protein)
>>> my_protein.reverse_complement()
Traceback (most recent call last):
...
ValueError: Proteins do not have complements!
"""
# Use -1 stride/step to reverse the complement
return self.complement()[::-1]
def transcribe(self):
"""Return the RNA sequence from a DNA sequence by creating a new Seq object.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG",
... IUPAC.unambiguous_dna)
>>> coding_dna
Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA())
>>> coding_dna.transcribe()
Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA())
Trying to transcribe a protein or RNA sequence raises an exception:
>>> my_protein = Seq("MAIVMGR", IUPAC.protein)
>>> my_protein.transcribe()
Traceback (most recent call last):
...
ValueError: Proteins cannot be transcribed!
"""
base = Alphabet._get_base_alphabet(self.alphabet)
if isinstance(base, Alphabet.ProteinAlphabet):
raise ValueError("Proteins cannot be transcribed!")
if isinstance(base, Alphabet.RNAAlphabet):
raise ValueError("RNA cannot be transcribed!")
if self.alphabet == IUPAC.unambiguous_dna:
alphabet = IUPAC.unambiguous_rna
elif self.alphabet == IUPAC.ambiguous_dna:
alphabet = IUPAC.ambiguous_rna
else:
alphabet = Alphabet.generic_rna
return Seq(str(self).replace("T", "U").replace("t", "u"), alphabet)
def back_transcribe(self):
"""Return the DNA sequence from an RNA sequence by creating a 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!
"""
base = Alphabet._get_base_alphabet(self.alphabet)
if isinstance(base, Alphabet.ProteinAlphabet):
raise ValueError("Proteins cannot be back transcribed!")
if isinstance(base, 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 translate(
self, table="Standard", stop_symbol="*", to_stop=False, cds=False, gap=None
):
"""Turn a nucleotide sequence into a protein sequence by creating a new Seq object.
This method will translate DNA or RNA sequences, and those with a
nucleotide or generic alphabet. Trying to translate a protein
sequence raises an exception.
Arguments:
- table - Which codon table to use? This can be either a name
(string), an NCBI identifier (integer), or a CodonTable
object (useful for non-standard genetic codes). 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).
- cds - Boolean, indicates this is a complete CDS. If True,
this checks the sequence starts with a valid alternative start
codon (which will be translated as methionine, M), that the
sequence length is a multiple of three, and that there is a
single in frame stop codon at the end (this will be excluded
from the protein sequence, regardless of the to_stop option).
If these tests fail, an exception is raised.
- gap - Single character string to denote symbol used for gaps.
It will try to guess the gap character from the alphabet.
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())
In fact, GTG is an alternative start codon under NCBI table 2, meaning
this sequence could be a complete CDS:
>>> coding_dna.translate(table=2, cds=True)
Seq('MAIVMGRWKGAR', ExtendedIUPACProtein())
It isn't a valid CDS under NCBI table 1, due to both the start codon
and also the in frame stop codons:
>>> coding_dna.translate(table=1, cds=True)
Traceback (most recent call last):
...
Bio.Data.CodonTable.TranslationError: First codon 'GTG' is not a start codon
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())
When translating gapped sequences, the gap character is inferred from
the alphabet:
>>> from Bio.Alphabet import Gapped
>>> coding_dna3 = Seq("GTG---GCCATT", Gapped(IUPAC.unambiguous_dna))
>>> coding_dna3.translate()
Seq('V-AI', Gapped(ExtendedIUPACProtein(), '-'))
It is possible to pass the gap character when the alphabet is missing:
>>> coding_dna4 = Seq("GTG---GCCATT")
>>> coding_dna4.translate(gap='-')
Seq('V-AI', Gapped(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 - This does NOT behave like the python string's translate
method. For that use str(my_seq).translate(...) instead.
"""
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!")
try:
table_id = int(table)
except ValueError:
# Assume its a table name
if self.alphabet == IUPAC.unambiguous_dna:
# Will use standard IUPAC protein alphabet, no need for X
codon_table = CodonTable.unambiguous_dna_by_name[table]
elif self.alphabet == IUPAC.unambiguous_rna:
# Will use standard IUPAC protein alphabet, no need for X
codon_table = CodonTable.unambiguous_rna_by_name[table]
else:
# This will use the extended IUPAC protein alphabet with X etc.
# The same table can be used for RNA or DNA (we use this for
# translating strings).
codon_table = CodonTable.ambiguous_generic_by_name[table]
except (AttributeError, TypeError):
# Assume its a CodonTable object
if isinstance(table, CodonTable.CodonTable):
codon_table = table
else:
raise ValueError("Bad table argument")
else:
# Assume its a table ID
if self.alphabet == IUPAC.unambiguous_dna:
# Will use standard IUPAC protein alphabet, no need for X
codon_table = CodonTable.unambiguous_dna_by_id[table_id]
elif self.alphabet == IUPAC.unambiguous_rna:
# Will use standard IUPAC protein alphabet, no need for X
codon_table = CodonTable.unambiguous_rna_by_id[table_id]
else:
# This will use the extended IUPAC protein alphabet with X etc.
# The same table can be used for RNA or DNA (we use this for
# translating strings).
codon_table = CodonTable.ambiguous_generic_by_id[table_id]
# Deal with gaps for translation
if hasattr(self.alphabet, "gap_char"):
if not gap:
gap = self.alphabet.gap_char
elif gap != self.alphabet.gap_char:
raise ValueError(
"Gap {0!r} does not match {1!r} from alphabet".format(
gap, self.alphabet.gap_char
)
)
protein = _translate_str(
str(self), codon_table, stop_symbol, to_stop, cds, gap=gap
)
if gap and gap in protein:
alphabet = Alphabet.Gapped(codon_table.protein_alphabet, gap)
else:
alphabet = codon_table.protein_alphabet
if stop_symbol in protein:
alphabet = Alphabet.HasStopCodon(alphabet, stop_symbol)
return Seq(protein, alphabet)
def ungap(self, gap=None):
"""Return a copy of the sequence without the gap character(s).
The gap character can be specified in two ways - either as an explicit
argument, or via the sequence's alphabet. For example:
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_dna
>>> my_dna = Seq("-ATA--TGAAAT-TTGAAAA", generic_dna)
>>> my_dna
Seq('-ATA--TGAAAT-TTGAAAA', DNAAlphabet())
>>> my_dna.ungap("-")
Seq('ATATGAAATTTGAAAA', DNAAlphabet())
If the gap character is not given as an argument, it will be taken from
the sequence's alphabet (if defined). Notice that the returned
sequence's alphabet is adjusted since it no longer requires a gapped
alphabet:
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC, Gapped, HasStopCodon
>>> my_pro = Seq("MVVLE=AD*", HasStopCodon(Gapped(IUPAC.protein, "=")))
>>> my_pro
Seq('MVVLE=AD*', HasStopCodon(Gapped(IUPACProtein(), '='), '*'))
>>> my_pro.ungap()
Seq('MVVLEAD*', HasStopCodon(IUPACProtein(), '*'))
Or, with a simpler gapped DNA example:
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC, Gapped
>>> my_seq = Seq("CGGGTAG=AAAAAA", Gapped(IUPAC.unambiguous_dna, "="))
>>> my_seq
Seq('CGGGTAG=AAAAAA', Gapped(IUPACUnambiguousDNA(), '='))
>>> my_seq.ungap()
Seq('CGGGTAGAAAAAA', IUPACUnambiguousDNA())
As long as it is consistent with the alphabet, although it is
redundant, you can still supply the gap character as an argument to
this method:
>>> my_seq
Seq('CGGGTAG=AAAAAA', Gapped(IUPACUnambiguousDNA(), '='))
>>> my_seq.ungap("=")
Seq('CGGGTAGAAAAAA', IUPACUnambiguousDNA())
However, if the gap character given as the argument disagrees with that
declared in the alphabet, an exception is raised:
>>> my_seq
Seq('CGGGTAG=AAAAAA', Gapped(IUPACUnambiguousDNA(), '='))
>>> my_seq.ungap("-")
Traceback (most recent call last):
...
ValueError: Gap '-' does not match '=' from alphabet
Finally, if a gap character is not supplied, and the alphabet does not
define one, an exception is raised:
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import generic_dna
>>> my_dna = Seq("ATA--TGAAAT-TTGAAAA", generic_dna)
>>> my_dna
Seq('ATA--TGAAAT-TTGAAAA', DNAAlphabet())
>>> my_dna.ungap()
Traceback (most recent call last):
...
ValueError: Gap character not given and not defined in alphabet
"""
if hasattr(self.alphabet, "gap_char"):
if not gap:
gap = self.alphabet.gap_char
elif gap != self.alphabet.gap_char:
raise ValueError(
"Gap {0!r} does not match {1!r} from alphabet".format(
gap, self.alphabet.gap_char
)
)
alpha = Alphabet._ungap(self.alphabet)
elif not gap:
raise ValueError("Gap character not given and not defined in alphabet")
else:
alpha = self.alphabet # modify!
if len(gap) != 1 or not isinstance(gap, str):
raise ValueError("Unexpected gap character, {0!r}".format(gap))
return Seq(str(self).replace(gap, ""), alpha)
def join(self, other):
"""Return a merge of the sequences in other, spaced by the sequence from self.
Accepts all Seq objects and Strings as objects to be concatenated with the spacer
>>> concatenated = Seq('NNNNN').join([Seq("AAA"), Seq("TTT"), Seq("PPP")])
>>> concatenated
Seq('AAANNNNNTTTNNNNNPPP')
Throws error if other is not an iterable and if objects inside of the iterable
are not Seq or String objects
"""
if not isinstance(other, _Iterable): # doesn't detect single strings
raise ValueError("Input must be an iterable")
if isinstance(other, basestring):
raise ValueError("Input must be an iterable")
from Bio.SeqRecord import SeqRecord # Lazy to avoid circular imports
a = self.alphabet
for c in other:
if isinstance(c, SeqRecord):
raise TypeError("Iterable cannot contain SeqRecords")
elif hasattr(c, "alphabet"):
if a != c.alphabet:
if not Alphabet._check_type_compatible([a, c.alphabet]):
raise TypeError(
"Incompatible alphabets {0!r} and {1!r}".format(
a, c.alphabet
)
)
a = Alphabet._consensus_alphabet([a, c.alphabet])
elif not isinstance(c, basestring):
raise ValueError("Input must be an iterable of Seqs or Strings")
temp_data = str(self).join([str(z) for z in other])
return self.__class__(temp_data, a)
class UnknownSeq(Seq):
"""Read-only sequence object of known length but unknown contents.
If you have an unknown sequence, you can represent this with a normal
Seq object, for example:
>>> my_seq = Seq("N"*5)
>>> my_seq
Seq('NNNNN')
>>> len(my_seq)
5
>>> print(my_seq)
NNNNN
However, this is rather wasteful of memory (especially for large
sequences), which is where this class is most useful:
>>> unk_five = UnknownSeq(5)
>>> unk_five
UnknownSeq(5, character='?')
>>> len(unk_five)
5
>>> print(unk_five)
?????
You can add unknown sequence together, provided their alphabets and
characters are compatible, and get another memory saving UnknownSeq:
>>> unk_four = UnknownSeq(4)
>>> unk_four
UnknownSeq(4, character='?')
>>> unk_four + unk_five
UnknownSeq(9, character='?')
If the alphabet or characters don't match up, the addition gives an
ordinary Seq object:
>>> unk_nnnn = UnknownSeq(4, character="N")
>>> unk_nnnn
UnknownSeq(4, character='N')
>>> unk_nnnn + unk_four
Seq('NNNN????')
Combining with a real Seq gives a new Seq object:
>>> known_seq = Seq("ACGT")
>>> unk_four + known_seq
Seq('????ACGT')
>>> known_seq + unk_four
Seq('ACGT????')
"""
def __init__(self, length, alphabet=Alphabet.generic_alphabet, character=None):
"""Create a new UnknownSeq object.
If character is omitted, it is determined from the alphabet, "N" for
nucleotides, "X" for proteins, and "?" otherwise.
"""
self._length = int(length)
if self._length < 0:
# TODO - Block zero length UnknownSeq? You can just use a Seq!
raise ValueError("Length must not be negative.")
self.alphabet = alphabet
if character:
if len(character) != 1:
raise ValueError("character argument should be a single letter string.")
self._character = character
else:
base = Alphabet._get_base_alphabet(alphabet)
# TODO? Check the case of the letters in the alphabet?
# We may have to use "n" instead of "N" etc.
if isinstance(base, Alphabet.NucleotideAlphabet):
self._character = "N"
elif isinstance(base, Alphabet.ProteinAlphabet):
self._character = "X"
else:
self._character = "?"
def __len__(self):
"""Return the stated length of the unknown sequence."""
return self._length
def __str__(self):
"""Return the unknown sequence as full string of the given length."""
return self._character * self._length
def __repr__(self):
"""Return (truncated) representation of the sequence for debugging."""
if self.alphabet is Alphabet.generic_alphabet:
# Default used, we can omit it and simplify the representation
a = ""
else:
a = ", alphabet=%r" % self.alphabet
return "UnknownSeq({0}{1!s}, character={2!r})".format(
self._length, a, self._character
)
def __add__(self, other):
"""Add another sequence or string to this sequence.
Adding two UnknownSeq objects returns another UnknownSeq object
provided the character is the same and the alphabets are compatible.
>>> from Bio.Seq import UnknownSeq
>>> from Bio.Alphabet import generic_protein
>>> UnknownSeq(10, generic_protein) + UnknownSeq(5, generic_protein)
UnknownSeq(15, alphabet=ProteinAlphabet(), character='X')
If the characters differ, an UnknownSeq object cannot be used, so a
Seq object is returned:
>>> from Bio.Seq import UnknownSeq
>>> from Bio.Alphabet import generic_protein
>>> UnknownSeq(10, generic_protein) + UnknownSeq(5, generic_protein,
... character="x")
Seq('XXXXXXXXXXxxxxx', ProteinAlphabet())
If adding a string to an UnknownSeq, a new Seq is returned with the
same alphabet:
>>> from Bio.Seq import UnknownSeq
>>> from Bio.Alphabet import generic_protein
>>> UnknownSeq(5, generic_protein) + "LV"
Seq('XXXXXLV', ProteinAlphabet())
"""
if isinstance(other, UnknownSeq) and other._character == self._character:
# TODO - Check the alphabets match
return UnknownSeq(len(self) + len(other), self.alphabet, self._character)
# Offload to the base class...
return Seq(str(self), self.alphabet) + other
def __radd__(self, other):
"""Add a sequence on the left."""
# If other is an UnknownSeq, then __add__ would be called.
# Offload to the base class...
return other + Seq(str(self), self.alphabet)
def __mul__(self, other):
"""Multiply UnknownSeq by integer.
>>> from Bio.Seq import UnknownSeq
>>> from Bio.Alphabet import generic_dna
>>> UnknownSeq(3) * 2
UnknownSeq(6, character='?')
>>> UnknownSeq(3, generic_dna) * 2
UnknownSeq(6, alphabet=DNAAlphabet(), character='N')
"""
if not isinstance(other, int):
raise TypeError(
"can't multiply {} by non-int type".format(self.__class__.__name__)
)
return self.__class__(len(self) * other, self.alphabet)
def __rmul__(self, other):
"""Multiply integer by UnknownSeq.
>>> from Bio.Seq import UnknownSeq
>>> from Bio.Alphabet import generic_dna
>>> 2 * UnknownSeq(3)
UnknownSeq(6, character='?')
>>> 2 * UnknownSeq(3, generic_dna)
UnknownSeq(6, alphabet=DNAAlphabet(), character='N')
"""
if not isinstance(other, int):
raise TypeError(
"can't multiply {} by non-int type".format(self.__class__.__name__)
)
return self.__class__(len(self) * other, self.alphabet)
def __imul__(self, other):
"""Multiply UnknownSeq in-place.
Note although UnknownSeq is immutable, the in-place method is
included to match the behaviour for regular Python strings.
>>> from Bio.Seq import UnknownSeq
>>> from Bio.Alphabet import generic_dna
>>> seq = UnknownSeq(3, generic_dna)
>>> seq *= 2
>>> seq
UnknownSeq(6, alphabet=DNAAlphabet(), character='N')
"""
if not isinstance(other, int):
raise TypeError(
"can't multiply {} by non-int type".format(self.__class__.__name__)
)
return self.__class__(len(self) * other, self.alphabet)
def __getitem__(self, index):
"""Get a subsequence from the UnknownSeq object.
>>> unk = UnknownSeq(8, character="N")
>>> print(unk[:])
NNNNNNNN
>>> print(unk[5:3])
<BLANKLINE>
>>> print(unk[1:-1])
NNNNNN
>>> print(unk[1:-1:2])
NNN
"""
if isinstance(index, int):
# TODO - Check the bounds without wasting memory
return str(self)[index]
old_length = self._length
step = index.step
if step is None or step == 1:
# This calculates the length you'd get from ("N"*old_length)[index]
start = index.start
end = index.stop
if start is None:
start = 0
elif start < 0:
start = max(0, old_length + start)
elif start > old_length:
start = old_length
if end is None:
end = old_length
elif end < 0:
end = max(0, old_length + end)
elif end > old_length:
end = old_length
new_length = max(0, end - start)
elif step == 0:
raise ValueError("slice step cannot be zero")
else:
# TODO - handle step efficiently
new_length = len(("X" * old_length)[index])
# assert new_length == len(("X"*old_length)[index]), \
# (index, start, end, step, old_length,
# new_length, len(("X"*old_length)[index]))
return UnknownSeq(new_length, self.alphabet, self._character)
def count(self, sub, start=0, end=sys.maxsize):
"""Return a non-overlapping count, like that of a python string.
This behaves like the python string (and Seq object) method of the
same name, which does a non-overlapping count!
For an overlapping search use the newer count_overlap() method.
Returns an integer, the number of occurrences of substring
argument sub in the (sub)sequence given by [start:end].
Optional arguments start and end are interpreted as in slice
notation.
Arguments:
- sub - a string or another Seq object to look for
- start - optional integer, slice start
- end - optional integer, slice end
>>> "NNNN".count("N")
4
>>> Seq("NNNN").count("N")
4
>>> UnknownSeq(4, character="N").count("N")
4
>>> UnknownSeq(4, character="N").count("A")
0
>>> UnknownSeq(4, character="N").count("AA")
0
HOWEVER, please note because that python strings and Seq objects (and
MutableSeq objects) do a non-overlapping search, this may not give
the answer you expect:
>>> UnknownSeq(4, character="N").count("NN")
2
>>> UnknownSeq(4, character="N").count("NNN")
1
"""
sub_str = self._get_seq_str_and_check_alphabet(sub)
len_self, len_sub_str = self._length, len(sub_str)
# Handling case where substring not in self
if set(sub_str) != set(self._character):
return 0
# Setting None to the default arguments
if start is None:
start = 0
if end is None:
end = sys.maxsize
# Truncating start and end to max of self._length and min of -self._length
start = max(min(start, len_self), -len_self)
end = max(min(end, len_self), -len_self)
# Convert start and ends to positive indexes
if start < 0:
start += len_self
if end < 0:
end += len_self
# Handle case where end <= start (no negative step argument here)
# and case where len_sub_str is larger than the search space
if end <= start or (end - start) < len_sub_str:
return 0
# 'Normal' calculation
return (end - start) // len_sub_str
def count_overlap(self, sub, start=0, end=sys.maxsize):
"""Return an overlapping count.
For a non-overlapping search use the count() method.
Returns an integer, the number of occurrences of substring
argument sub in the (sub)sequence given by [start:end].
Optional arguments start and end are interpreted as in slice
notation.
Arguments:
- sub - a string or another Seq object to look for
- start - optional integer, slice start
- end - optional integer, slice end
e.g.
>>> from Bio.Seq import UnknownSeq
>>> UnknownSeq(4, character="N").count_overlap("NN")
3
>>> UnknownSeq(4, character="N").count_overlap("NNN")
2
Where substrings do not overlap, should behave the same as
the count() method:
>>> UnknownSeq(4, character="N").count_overlap("N")
4
>>> UnknownSeq(4, character="N").count_overlap("N") == UnknownSeq(4, character="N").count("N")
True
>>> UnknownSeq(4, character="N").count_overlap("A")
0
>>> UnknownSeq(4, character="N").count_overlap("A") == UnknownSeq(4, character="N").count("A")
True
>>> UnknownSeq(4, character="N").count_overlap("AA")
0
>>> UnknownSeq(4, character="N").count_overlap("AA") == UnknownSeq(4, character="N").count("AA")
True
"""
sub_str = self._get_seq_str_and_check_alphabet(sub)
len_self, len_sub_str = self._length, len(sub_str)
# Handling case where substring not in self
if set(sub_str) != set(self._character):
return 0
# Setting None to the default arguments
if start is None:
start = 0
if end is None:
end = sys.maxsize
# Truncating start and end to max of self._length and min of -self._length
start = max(min(start, len_self), -len_self)
end = max(min(end, len_self), -len_self)
# Convert start and ends to positive indexes
if start < 0:
start += len_self
if end < 0:
end += len_self
# Handle case where end <= start (no negative step argument here)
# and case where len_sub_str is larger than the search space
if end <= start or (end - start) < len_sub_str:
return 0
# 'Normal' calculation
return end - start - len_sub_str + 1
def complement(self):
"""Return the complement of an unknown nucleotide equals itself.
>>> my_nuc = UnknownSeq(8)
>>> my_nuc
UnknownSeq(8, character='?')
>>> print(my_nuc)
????????
>>> my_nuc.complement()
UnknownSeq(8, character='?')
>>> print(my_nuc.complement())
????????
"""
if isinstance(
Alphabet._get_base_alphabet(self.alphabet), Alphabet.ProteinAlphabet
):
raise ValueError("Proteins do not have complements!")
return self
def reverse_complement(self):
"""Return the reverse complement of an unknown sequence.
The reverse complement of an unknown nucleotide equals itself:
>>> from Bio.Seq import UnknownSeq
>>> from Bio.Alphabet import generic_dna
>>> example = UnknownSeq(6, generic_dna)
>>> print(example)
NNNNNN
>>> print(example.reverse_complement())
NNNNNN
"""
if isinstance(
Alphabet._get_base_alphabet(self.alphabet), Alphabet.ProteinAlphabet
):
raise ValueError("Proteins do not have complements!")
return self
def transcribe(self):
"""Return an unknown RNA sequence from an unknown DNA sequence.
>>> my_dna = UnknownSeq(10, character="N")
>>> my_dna
UnknownSeq(10, character='N')
>>> print(my_dna)
NNNNNNNNNN
>>> my_rna = my_dna.transcribe()
>>> my_rna
UnknownSeq(10, alphabet=RNAAlphabet(), character='N')
>>> print(my_rna)
NNNNNNNNNN
"""
# Offload the alphabet stuff
s = Seq(self._character, self.alphabet).transcribe()
return UnknownSeq(self._length, s.alphabet, self._character)
def back_transcribe(self):
"""Return an unknown DNA sequence from an unknown RNA sequence.
>>> my_rna = UnknownSeq(20, character="N")
>>> my_rna
UnknownSeq(20, character='N')
>>> print(my_rna)
NNNNNNNNNNNNNNNNNNNN
>>> my_dna = my_rna.back_transcribe()
>>> my_dna
UnknownSeq(20, alphabet=DNAAlphabet(), character='N')
>>> print(my_dna)
NNNNNNNNNNNNNNNNNNNN
"""
# Offload the alphabet stuff
s = Seq(self._character, self.alphabet).back_transcribe()
return UnknownSeq(self._length, s.alphabet, self._character)
def upper(self):
"""Return an upper case copy of the sequence.
>>> from Bio.Alphabet import generic_dna
>>> from Bio.Seq import UnknownSeq
>>> my_seq = UnknownSeq(20, generic_dna, character="n")
>>> my_seq
UnknownSeq(20, alphabet=DNAAlphabet(), character='n')
>>> print(my_seq)
nnnnnnnnnnnnnnnnnnnn
>>> my_seq.upper()
UnknownSeq(20, alphabet=DNAAlphabet(), character='N')
>>> print(my_seq.upper())
NNNNNNNNNNNNNNNNNNNN
This will adjust the alphabet if required. See also the lower method.
"""
return UnknownSeq(self._length, self.alphabet._upper(), self._character.upper())
def lower(self):
"""Return a lower case copy of the sequence.
This will adjust the alphabet if required:
>>> from Bio.Alphabet import IUPAC
>>> from Bio.Seq import UnknownSeq
>>> my_seq = UnknownSeq(20, IUPAC.extended_protein)
>>> my_seq
UnknownSeq(20, alphabet=ExtendedIUPACProtein(), character='X')
>>> print(my_seq)
XXXXXXXXXXXXXXXXXXXX
>>> my_seq.lower()
UnknownSeq(20, alphabet=ProteinAlphabet(), character='x')
>>> print(my_seq.lower())
xxxxxxxxxxxxxxxxxxxx
See also the upper method.
"""
return UnknownSeq(self._length, self.alphabet._lower(), self._character.lower())
def translate(self, **kwargs):
"""Translate an unknown nucleotide sequence into an unknown protein.
e.g.
>>> my_seq = UnknownSeq(9, character="N")
>>> print(my_seq)
NNNNNNNNN
>>> my_protein = my_seq.translate()
>>> my_protein
UnknownSeq(3, alphabet=ProteinAlphabet(), character='X')
>>> print(my_protein)
XXX
In comparison, using a normal Seq object:
>>> my_seq = Seq("NNNNNNNNN")
>>> print(my_seq)
NNNNNNNNN
>>> my_protein = my_seq.translate()
>>> my_protein
Seq('XXX', ExtendedIUPACProtein())
>>> print(my_protein)
XXX
"""
if isinstance(
Alphabet._get_base_alphabet(self.alphabet), Alphabet.ProteinAlphabet
):
raise ValueError("Proteins cannot be translated!")
return UnknownSeq(self._length // 3, Alphabet.generic_protein, "X")
def ungap(self, gap=None):
"""Return a copy of the sequence without the gap character(s).
The gap character can be specified in two ways - either as an explicit
argument, or via the sequence's alphabet. For example:
>>> from Bio.Seq import UnknownSeq
>>> from Bio.Alphabet import Gapped, generic_dna
>>> my_dna = UnknownSeq(20, Gapped(generic_dna, "-"))
>>> my_dna
UnknownSeq(20, alphabet=Gapped(DNAAlphabet(), '-'), character='N')
>>> my_dna.ungap()
UnknownSeq(20, alphabet=DNAAlphabet(), character='N')
>>> my_dna.ungap("-")
UnknownSeq(20, alphabet=DNAAlphabet(), character='N')
If the UnknownSeq is using the gap character, then an empty Seq is
returned:
>>> my_gap = UnknownSeq(20, Gapped(generic_dna, "-"), character="-")
>>> my_gap
UnknownSeq(20, alphabet=Gapped(DNAAlphabet(), '-'), character='-')
>>> my_gap.ungap()
Seq('', DNAAlphabet())
>>> my_gap.ungap("-")
Seq('', DNAAlphabet())
Notice that the returned sequence's alphabet is adjusted to remove any
explicit gap character declaration.
"""
# Offload the alphabet stuff
s = Seq(self._character, self.alphabet).ungap(gap)
if s:
return UnknownSeq(self._length, s.alphabet, self._character)
else:
return Seq("", s.alphabet)
def join(self, other):
"""Return a merge of the sequences in other, spaced by the sequence from self.
Accepts Seq/UnknownSeq objects and Strings as objects to be concatenated with
the spacer
>>> concatenated = UnknownSeq(5).join([Seq("AAA"), Seq("TTT"), Seq("PPP")])
>>> concatenated
Seq('AAA?????TTT?????PPP')
Throws error if other is not an iterable and if objects inside of the iterable
are not Seq/UnknownSeq or String objects.
Will only return an UnknownSeq object of all of the objects to be joined are
also UnknownSeqs with the same character as the spacer, similar to how the
addition of an UnknownSeq and another UnknownSeq would work.
"""
if not isinstance(other, collections.Iterable): # doesn't detect single strings
raise ValueError("Input must be an iterable")
if isinstance(other, basestring):
raise ValueError("Input must be an iterable")
from Bio.SeqRecord import SeqRecord # Lazy to avoid circular imports
a = self.alphabet
type_is_unknown = True
for c in other:
if isinstance(c, SeqRecord):
raise TypeError("Iterable cannot contain SeqRecords")
elif hasattr(c, "alphabet"):
if a != c.alphabet:
if not Alphabet._check_type_compatible([a, c.alphabet]):
raise TypeError(
"Incompatible alphabets {0!r} and {1!r}".format(
a, c.alphabet
)
)
a = Alphabet._consensus_alphabet([a, c.alphabet])
if not isinstance(c, UnknownSeq):
type_is_unknown = False
elif isinstance(c, basestring):
type_is_unknown = False
else:
raise ValueError("Input must be an iterable of Seqs or Strings")
temp_data = str(self).join([str(z) for z in other])
if (
temp_data.count(self._character) == len(temp_data)
and type_is_unknown is True
):
return self.__class__(len(temp_data), a, self._character)
return Seq(temp_data, a)
class MutableSeq(object):
"""An editable sequence object (with an alphabet).
Unlike normal python strings and our basic sequence object (the Seq class)
which are immutable, the MutableSeq lets you edit the sequence in place.
However, this means you cannot use a MutableSeq object as a dictionary key.
>>> from Bio.Seq import MutableSeq
>>> from Bio.Alphabet import generic_dna
>>> my_seq = MutableSeq("ACTCGTCGTCG", generic_dna)
>>> my_seq
MutableSeq('ACTCGTCGTCG', DNAAlphabet())
>>> my_seq[5]
'T'
>>> my_seq[5] = "A"
>>> my_seq
MutableSeq('ACTCGACGTCG', DNAAlphabet())
>>> my_seq[5]
'A'
>>> my_seq[5:8] = "NNN"
>>> my_seq
MutableSeq('ACTCGNNNTCG', DNAAlphabet())
>>> len(my_seq)
11
Note that the MutableSeq object does not support as many string-like
or biological methods as the Seq object.
"""
def __init__(self, data, alphabet=Alphabet.generic_alphabet):
"""Initialize the class."""
if sys.version_info[0] == 3:
self.array_indicator = "u"
else:
self.array_indicator = "c"
if isinstance(data, str): # TODO - What about unicode?
self.data = array.array(self.array_indicator, data)
elif isinstance(data, (Seq, int, float)):
raise TypeError(
"The sequence data given to a MutableSeq object "
"should be a string or an array (not a Seq object etc)"
)
else:
self.data = data # assumes the input is an array
self.alphabet = alphabet
def __repr__(self):
"""Return (truncated) representation of the sequence for debugging."""
if self.alphabet is Alphabet.generic_alphabet:
# Default used, we can omit it and simplify the representation
a = ""
else:
a = ", %r" % self.alphabet
if len(self) > 60:
# Shows the last three letters as it is often useful to see if
# there is a stop codon at the end of a sequence.
# Note total length is 54+3+3=60
return "{0}('{1}...{2}'{3!s})".format(
self.__class__.__name__, str(self[:54]), str(self[-3:]), a
)
else:
return "{0}('{1}'{2!s})".format(self.__class__.__name__, str(self), a)
def __str__(self):
"""Return the full sequence as a python string.
Note that Biopython 1.44 and earlier would give a truncated
version of repr(my_seq) for str(my_seq). If you are writing code
which needs to be backwards compatible with old Biopython, you
should continue to use my_seq.tostring() rather than str(my_seq).
"""
# See test_GAQueens.py for an historic usage of a non-string alphabet!
return "".join(self.data)
def __eq__(self, other):
"""Compare the sequence to another sequence or a string (README).
Currently if compared to another sequence the alphabets must be
compatible. Comparing DNA to RNA, or Nucleotide to Protein will raise
an exception. Otherwise only the sequence itself is compared, not the
precise alphabet.
A future release of Biopython will change this (and the Seq object etc)
to use simple string comparison. The plan is that comparing sequences
with incompatible alphabets (e.g. DNA to RNA) will trigger a warning
but not an exception.
During this transition period, please just do explicit comparisons:
>>> seq1 = MutableSeq("ACGT")
>>> seq2 = MutableSeq("ACGT")
>>> id(seq1) == id(seq2)
False
>>> str(seq1) == str(seq2)
True
Biopython now does:
>>> seq1 == seq2
True
>>> seq1 == Seq("ACGT")
True
>>> seq1 == "ACGT"
True
"""
if hasattr(other, "alphabet"):
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
warnings.warn(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
),
BiopythonWarning,
)
if isinstance(other, MutableSeq):
return self.data == other.data
return str(self) == str(other)
def __ne__(self, other):
"""Implement the not-equal operand."""
# Seem to require this method for Python 2 but not needed on Python 3?
return not (self == other)
def __lt__(self, other):
"""Implement the less-than operand."""
if hasattr(other, "alphabet"):
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
warnings.warn(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
),
BiopythonWarning,
)
if isinstance(other, MutableSeq):
return self.data < other.data
if isinstance(other, (str, Seq, UnknownSeq)):
return str(self) < str(other)
raise TypeError(
"'<' not supported between instances of '{}' and '{}'".format(
type(self).__name__, type(other).__name__
)
)
def __le__(self, other):
"""Implement the less-than or equal operand."""
if hasattr(other, "alphabet"):
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
warnings.warn(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
),
BiopythonWarning,
)
if isinstance(other, MutableSeq):
return self.data <= other.data
if isinstance(other, (str, Seq, UnknownSeq)):
return str(self) <= str(other)
raise TypeError(
"'<=' not supported between instances of '{}' and '{}'".format(
type(self).__name__, type(other).__name__
)
)
def __gt__(self, other):
"""Implement the greater-than operand."""
if hasattr(other, "alphabet"):
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
warnings.warn(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
),
BiopythonWarning,
)
if isinstance(other, MutableSeq):
return self.data > other.data
if isinstance(other, (str, Seq, UnknownSeq)):
return str(self) > str(other)
raise TypeError(
"'>' not supported between instances of '{}' and '{}'".format(
type(self).__name__, type(other).__name__
)
)
def __ge__(self, other):
"""Implement the greater-than or equal operand."""
if hasattr(other, "alphabet"):
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
warnings.warn(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
),
BiopythonWarning,
)
if isinstance(other, MutableSeq):
return self.data >= other.data
if isinstance(other, (str, Seq, UnknownSeq)):
return str(self) >= str(other)
raise TypeError(
"'>=' not supported between instances of '{}' and '{}'".format(
type(self).__name__, type(other).__name__
)
)
def __len__(self):
"""Return the length of the sequence, use len(my_seq)."""
return len(self.data)
def __getitem__(self, index):
"""Return a subsequence of single letter, use my_seq[index].
>>> my_seq = MutableSeq('ACTCGACGTCG')
>>> my_seq[5]
'A'
"""
# Note since Python 2.0, __getslice__ is deprecated
# and __getitem__ is used instead.
# See http://docs.python.org/ref/sequence-methods.html
if isinstance(index, int):
# Return a single letter as a string
return self.data[index]
else:
# Return the (sub)sequence as another Seq object
return MutableSeq(self.data[index], self.alphabet)
def __setitem__(self, index, value):
"""Set a subsequence of single letter via value parameter.
>>> my_seq = MutableSeq('ACTCGACGTCG')
>>> my_seq[0] = 'T'
>>> my_seq
MutableSeq('TCTCGACGTCG')
"""
# Note since Python 2.0, __setslice__ is deprecated
# and __setitem__ is used instead.
# See http://docs.python.org/ref/sequence-methods.html
if isinstance(index, int):
# Replacing a single letter with a new string
self.data[index] = value
else:
# Replacing a sub-sequence
if isinstance(value, MutableSeq):
self.data[index] = value.data
elif isinstance(value, type(self.data)):
self.data[index] = value
else:
self.data[index] = array.array(self.array_indicator, str(value))
def __delitem__(self, index):
"""Delete a subsequence of single letter.
>>> my_seq = MutableSeq('ACTCGACGTCG')
>>> del my_seq[0]
>>> my_seq
MutableSeq('CTCGACGTCG')
"""
# Note since Python 2.0, __delslice__ is deprecated
# and __delitem__ is used instead.
# See http://docs.python.org/ref/sequence-methods.html
# Could be deleting a single letter, or a slice
del self.data[index]
def __add__(self, other):
"""Add another sequence or string to this sequence.
Returns a new MutableSeq object.
"""
if hasattr(other, "alphabet"):
# other should be a Seq or a MutableSeq
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
raise TypeError(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
)
)
# They should be the same sequence type (or one of them is generic)
a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet])
if isinstance(other, MutableSeq):
# See test_GAQueens.py for an historic usage of a non-string
# alphabet! Adding the arrays should support this.
return self.__class__(self.data + other.data, a)
else:
return self.__class__(str(self) + str(other), a)
elif isinstance(other, basestring):
# other is a plain string - use the current alphabet
return self.__class__(str(self) + str(other), self.alphabet)
else:
raise TypeError
def __radd__(self, other):
"""Add a sequence on the left.
>>> from Bio.Seq import MutableSeq
>>> from Bio.Alphabet import generic_protein
>>> "LV" + MutableSeq("MELKI", generic_protein)
MutableSeq('LVMELKI', ProteinAlphabet())
"""
if hasattr(other, "alphabet"):
# other should be a Seq or a MutableSeq
if not Alphabet._check_type_compatible([self.alphabet, other.alphabet]):
raise TypeError(
"Incompatible alphabets {0!r} and {1!r}".format(
self.alphabet, other.alphabet
)
)
# They should be the same sequence type (or one of them is generic)
a = Alphabet._consensus_alphabet([self.alphabet, other.alphabet])
if isinstance(other, MutableSeq):
# See test_GAQueens.py for an historic usage of a non-string
# alphabet! Adding the arrays should support this.
return self.__class__(other.data + self.data, a)
else:
return self.__class__(str(other) + str(self), a)
elif isinstance(other, basestring):
# other is a plain string - use the current alphabet
return self.__class__(str(other) + str(self), self.alphabet)
else:
raise TypeError
def __mul__(self, other):
"""Multiply MutableSeq by integer.
Note this is not in-place and returns a new object,
matching native Python list multiplication.
>>> from Bio.Seq import MutableSeq
>>> from Bio.Alphabet import generic_dna
>>> MutableSeq('ATG') * 2
MutableSeq('ATGATG')
>>> MutableSeq('ATG', generic_dna) * 2
MutableSeq('ATGATG', DNAAlphabet())
"""
if not isinstance(other, int):
raise TypeError(
"can't multiply {} by non-int type".format(self.__class__.__name__)
)
return self.__class__(self.data * other, self.alphabet)
def __rmul__(self, other):
"""Multiply integer by MutableSeq.
Note this is not in-place and returns a new object,
matching native Python list multiplication.
>>> from Bio.Seq import MutableSeq
>>> from Bio.Alphabet import generic_dna
>>> 2 * MutableSeq('ATG')
MutableSeq('ATGATG')
>>> 2 * MutableSeq('ATG', generic_dna)
MutableSeq('ATGATG', DNAAlphabet())
"""
if not isinstance(other, int):
raise TypeError(
"can't multiply {} by non-int type".format(self.__class__.__name__)
)
return self.__class__(self.data * other, self.alphabet)
def __imul__(self, other):
"""Multiply MutableSeq in-place.
>>> from Bio.Seq import MutableSeq
>>> from Bio.Alphabet import generic_dna
>>> seq = MutableSeq('ATG', generic_dna)
>>> seq *= 2
>>> seq
MutableSeq('ATGATG', DNAAlphabet())
"""
if not isinstance(other, int):
raise TypeError(
"can't multiply {} by non-int type".format(self.__class__.__name__)
)
return self.__class__(self.data * other, self.alphabet)
def append(self, c):
"""Add a subsequence to the mutable sequence object.
>>> my_seq = MutableSeq('ACTCGACGTCG')
>>> my_seq.append('A')
>>> my_seq
MutableSeq('ACTCGACGTCGA')
No return value.
"""
self.data.append(c)
def insert(self, i, c):
"""Add a subsequence to the mutable sequence object at a given index.
>>> my_seq = MutableSeq('ACTCGACGTCG')
>>> my_seq.insert(0,'A')
>>> my_seq
MutableSeq('AACTCGACGTCG')
>>> my_seq.insert(8,'G')
>>> my_seq
MutableSeq('AACTCGACGGTCG')
No return value.
"""
self.data.insert(i, c)
def pop(self, i=(-1)):
"""Remove a subsequence of a single letter at given index.
>>> my_seq = MutableSeq('ACTCGACGTCG')
>>> my_seq.pop()
'G'
>>> my_seq
MutableSeq('ACTCGACGTC')
>>> my_seq.pop()
'C'
>>> my_seq
MutableSeq('ACTCGACGT')
Returns the last character of the sequence.
"""
c = self.data[i]
del self.data[i]
return c
def remove(self, item):
"""Remove a subsequence of a single letter from mutable sequence.
>>> my_seq = MutableSeq('ACTCGACGTCG')
>>> my_seq.remove('C')
>>> my_seq
MutableSeq('ATCGACGTCG')
>>> my_seq.remove('A')
>>> my_seq
MutableSeq('TCGACGTCG')
No return value.
"""
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, sub, start=0, end=sys.maxsize):
"""Return a non-overlapping count, like that of a python string.
This behaves like the python string method of the same name,
which does a non-overlapping count!
For an overlapping search use the newer count_overlap() method.
Returns an integer, the number of occurrences of substring
argument sub in the (sub)sequence given by [start:end].
Optional arguments start and end are interpreted as in slice
notation.
Arguments:
- sub - a string or another Seq object to look for
- start - optional integer, slice start
- end - optional integer, slice end
e.g.
>>> from Bio.Seq import MutableSeq
>>> my_mseq = MutableSeq("AAAATGA")
>>> print(my_mseq.count("A"))
5
>>> print(my_mseq.count("ATG"))
1
>>> print(my_mseq.count(Seq("AT")))
1
>>> print(my_mseq.count("AT", 2, -1))
1
HOWEVER, please note because that python strings, Seq objects and
MutableSeq objects do a non-overlapping search, this may not give
the answer you expect:
>>> "AAAA".count("AA")
2
>>> print(MutableSeq("AAAA").count("AA"))
2
An overlapping search would give the answer as three!
"""
try:
# TODO - Should we check the alphabet?
search = str(sub)
except AttributeError:
search = sub
if not isinstance(search, basestring):
raise TypeError("expected a string, Seq or MutableSeq")
if len(search) == 1:
# Try and be efficient and work directly from the array.
count = 0
for c in self.data[start:end]:
if c == search:
count += 1
return count
else:
# TODO - Can we do this more efficiently?
return str(self).count(search, start, end)
def count_overlap(self, sub, start=0, end=sys.maxsize):
"""Return an overlapping count.
For a non-overlapping search use the count() method.
Returns an integer, the number of occurrences of substring
argument sub in the (sub)sequence given by [start:end].
Optional arguments start and end are interpreted as in slice
notation.
Arguments:
- sub - a string or another Seq object to look for
- start - optional integer, slice start
- end - optional integer, slice end
e.g.
>>> from Bio.Seq import MutableSeq
>>> print(MutableSeq("AAAA").count_overlap("AA"))
3
>>> print(MutableSeq("ATATATATA").count_overlap("ATA"))
4
>>> print(MutableSeq("ATATATATA").count_overlap("ATA", 3, -1))
1
Where substrings do not overlap, should behave the same as
the count() method:
>>> from Bio.Seq import MutableSeq
>>> my_mseq = MutableSeq("AAAATGA")
>>> print(my_mseq.count_overlap("A"))
5
>>> my_mseq.count_overlap("A") == my_mseq.count("A")
True
>>> print(my_mseq.count_overlap("ATG"))
1
>>> my_mseq.count_overlap("ATG") == my_mseq.count("ATG")
True
>>> print(my_mseq.count_overlap(Seq("AT")))
1
>>> my_mseq.count_overlap(Seq("AT")) == my_mseq.count(Seq("AT"))
True
>>> print(my_mseq.count_overlap("AT", 2, -1))
1
>>> my_mseq.count_overlap("AT", 2, -1) == my_mseq.count("AT", 2, -1)
True
HOWEVER, do not use this method for such cases because the
count() method is much for efficient.
"""
# The implementation is currently identical to that of
# Seq.count_overlap() apart from the definition of sub_str
sub_str = str(sub)
self_str = str(self)
overlap_count = 0
while True:
start = self_str.find(sub_str, start, end) + 1
if start != 0:
overlap_count += 1
else:
return overlap_count
def index(self, item):
"""Return first occurrence position of a single entry (i.e. letter).
>>> my_seq = MutableSeq("ACTCGACGTCG")
>>> my_seq.index("A")
0
>>> my_seq.index("T")
2
>>> my_seq.index(Seq("T"))
2
Note unlike a Biopython Seq object, or Python string, multi-letter
subsequences are not supported. Instead this acts like an array or
a list of the entries. There is therefore no ``.rindex()`` method.
"""
# TODO?: return self.data.index(i)
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):
"""Modify the mutable sequence to reverse itself.
No return value.
"""
self.data.reverse()
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
mixed = d.copy() # We're going to edit this to be mixed case!
mixed.update((x.lower(), y.lower()) for x, y in d.items())
self.data = [mixed[_] for _ in self.data]
self.data = array.array(self.array_indicator, self.data)
def reverse_complement(self):
"""Modify the mutable sequence to take on its reverse complement.
Trying to reverse complement a protein sequence raises an exception.
No return value.
"""
self.complement()
self.data.reverse()
def extend(self, other):
"""Add a sequence to the original mutable sequence object.
>>> my_seq = MutableSeq('ACTCGACGTCG')
>>> my_seq.extend('A')
>>> my_seq
MutableSeq('ACTCGACGTCGA')
>>> my_seq.extend('TTT')
>>> my_seq
MutableSeq('ACTCGACGTCGATTT')
No return value.
"""
if isinstance(other, MutableSeq):
for c in other.data:
self.data.append(c)
else:
for c in other:
self.data.append(c)
def toseq(self):
"""Return the full sequence as a new immutable Seq object.
>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> my_mseq = MutableSeq("MKQHKAMIVALIVICITAVVAAL",
... IUPAC.protein)
>>> my_mseq
MutableSeq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
>>> my_mseq.toseq()
Seq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein())
Note that the alphabet is preserved.
"""
return Seq("".join(self.data), self.alphabet)
def join(self, other):
"""Return a merge of the sequences in other, spaced by the sequence from self.
Accepts all Seq objects and Strings as objects to be concatenated with the spacer
>>> concatenated = MutableSeq('NNNNN').join([Seq("AAA"), Seq("TTT"), Seq("PPP")])
>>> concatenated
Seq('AAANNNNNTTTNNNNNPPP')
Throws error if other is not an iterable and if objects inside of the iterable
are not Seq or String objects
"""
seq_joined = self.toseq().join(
other
) # returns Seq object instead of MutableSeq
return seq_joined
# 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):
"""Transcribe a DNA sequence into RNA.
If given a string, returns a new string object.
Given a Seq or MutableSeq, returns a new Seq object with an RNA alphabet.
Trying to transcribe a protein or RNA sequence raises an exception.
e.g.
>>> transcribe("ACTGN")
'ACUGN'
"""
if isinstance(dna, Seq):
return dna.transcribe()
elif isinstance(dna, MutableSeq):
return dna.toseq().transcribe()
else:
return dna.replace("T", "U").replace("t", "u")
def back_transcribe(rna):
"""Return the RNA sequence back-transcribed into DNA.
If given a string, returns a new string object.
Given a Seq or MutableSeq, returns a new Seq object with an RNA alphabet.
Trying to transcribe a protein or DNA sequence raises an exception.
e.g.
>>> back_transcribe("ACUGN")
'ACTGN'
"""
if isinstance(rna, Seq):
return rna.back_transcribe()
elif isinstance(rna, MutableSeq):
return rna.toseq().back_transcribe()
else:
return rna.replace("U", "T").replace("u", "t")
def _translate_str(
sequence, table, stop_symbol="*", to_stop=False, cds=False, pos_stop="X", gap=None
):
"""Translate nucleotide string into a protein string (PRIVATE).
Arguments:
- sequence - a string
- table - a CodonTable object (NOT a table name or id number)
- stop_symbol - a single character string, what to use for terminators.
- to_stop - boolean, should translation terminate at the first
in frame stop codon? If there is no in-frame stop codon
then translation continues to the end.
- pos_stop - a single character string for a possible stop codon
(e.g. TAN or NNN)
- cds - Boolean, indicates this is a complete CDS. If True, this
checks the sequence starts with a valid alternative start
codon (which will be translated as methionine, M), that the
sequence length is a multiple of three, and that there is a
single in frame stop codon at the end (this will be excluded
from the protein sequence, regardless of the to_stop option).
If these tests fail, an exception is raised.
- gap - Single character string to denote symbol used for gaps.
Defaults to None.
Returns a string.
e.g.
>>> from Bio.Data import CodonTable
>>> table = CodonTable.ambiguous_dna_by_id[1]
>>> _translate_str("AAA", table)
'K'
>>> _translate_str("TAR", table)
'*'
>>> _translate_str("TAN", table)
'X'
>>> _translate_str("TAN", table, pos_stop="@")
'@'
>>> _translate_str("TA?", table)
Traceback (most recent call last):
...
Bio.Data.CodonTable.TranslationError: Codon 'TA?' is invalid
In a change to older versions of Biopython, partial codons are now
always regarded as an error (previously only checked if cds=True)
and will trigger a warning (likely to become an exception in a
future release).
If **cds=True**, the start and stop codons are checked, and the start
codon will be translated at methionine. The sequence must be an
while number of codons.
>>> _translate_str("ATGCCCTAG", table, cds=True)
'MP'
>>> _translate_str("AAACCCTAG", table, cds=True)
Traceback (most recent call last):
...
Bio.Data.CodonTable.TranslationError: First codon 'AAA' is not a start codon
>>> _translate_str("ATGCCCTAGCCCTAG", table, cds=True)
Traceback (most recent call last):
...
Bio.Data.CodonTable.TranslationError: Extra in frame stop codon found.
"""
sequence = sequence.upper()
amino_acids = []
forward_table = table.forward_table
stop_codons = table.stop_codons
if table.nucleotide_alphabet.letters is not None:
valid_letters = set(table.nucleotide_alphabet.letters.upper())
else:
# Assume the worst case, ambiguous DNA or RNA:
valid_letters = set(
_ambiguous_dna_letters.upper() + _ambiguous_rna_letters.upper()
)
n = len(sequence)
# Check for tables with 'ambiguous' (dual-coding) stop codons:
dual_coding = [c for c in stop_codons if c in forward_table]
if dual_coding:
c = dual_coding[0]
if to_stop:
raise ValueError(
"You cannot use 'to_stop=True' with this table "
"as it contains {} codon(s) which can be both "
" STOP and an amino acid (e.g. '{}' -> '{}' or "
"STOP).".format(len(dual_coding), c, forward_table[c])
)
warnings.warn(
"This table contains {} codon(s) which code(s) for both "
"STOP and an amino acid (e.g. '{}' -> '{}' or STOP). "
"Such codons will be translated as amino acid.".format(
len(dual_coding), c, forward_table[c]
),
BiopythonWarning,
)
if cds:
if str(sequence[:3]).upper() not in table.start_codons:
raise CodonTable.TranslationError(
"First codon '{0}' is not a start codon".format(sequence[:3])
)
if n % 3 != 0:
raise CodonTable.TranslationError(
"Sequence length {0} is not a multiple of three".format(n)
)
if str(sequence[-3:]).upper() not in stop_codons:
raise CodonTable.TranslationError(
"Final codon '{0}' is not a stop codon".format(sequence[-3:])
)
# Don't translate the stop symbol, and manually translate the M
sequence = sequence[3:-3]
n -= 6
amino_acids = ["M"]
elif n % 3 != 0:
warnings.warn(
"Partial codon, len(sequence) not a multiple of three. "
"Explicitly trim the sequence or add trailing N before "
"translation. This may become an error in future.",
BiopythonWarning,
)
if gap is not None:
if not isinstance(gap, basestring):
raise TypeError("Gap character should be a single character string.")
elif len(gap) > 1:
raise ValueError("Gap character should be a single character string.")
for i in range(0, n - n % 3, 3):
codon = sequence[i : i + 3]
try:
amino_acids.append(forward_table[codon])
except (KeyError, CodonTable.TranslationError):
if codon in table.stop_codons:
if cds:
raise CodonTable.TranslationError(
"Extra in frame stop codon found."
)
if to_stop:
break
amino_acids.append(stop_symbol)
elif valid_letters.issuperset(set(codon)):
# Possible stop codon (e.g. NNN or TAN)
amino_acids.append(pos_stop)
elif gap is not None and codon == gap * 3:
# Gapped translation
amino_acids.append(gap)
else:
raise CodonTable.TranslationError(
"Codon '{0}' is invalid".format(codon)
)
return "".join(amino_acids)
def translate(
sequence, table="Standard", stop_symbol="*", to_stop=False, cds=False, gap=None
):
"""Translate a nucleotide sequence into amino acids.
If given a string, returns a new string object. Given a Seq or
MutableSeq, returns a Seq object with a protein alphabet.
Arguments:
- table - Which codon table to use? This can be either a name
(string), an NCBI identifier (integer), or a CodonTable object
(useful for non-standard genetic codes). Defaults to the "Standard"
table.
- stop_symbol - Single character string, what to use for any
terminators, 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).
- cds - Boolean, indicates this is a complete CDS. If True, this
checks the sequence starts with a valid alternative start
codon (which will be translated as methionine, M), that the
sequence length is a multiple of three, and that there is a
single in frame stop codon at the end (this will be excluded
from the protein sequence, regardless of the to_stop option).
If these tests fail, an exception is raised.
- gap - Single character string to denote symbol used for gaps.
Defaults to None.
A simple string example using the default (standard) genetic code:
>>> coding_dna = "GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG"
>>> translate(coding_dna)
'VAIVMGR*KGAR*'
>>> translate(coding_dna, stop_symbol="@")
'VAIVMGR@KGAR@'
>>> translate(coding_dna, to_stop=True)
'VAIVMGR'
Now using NCBI table 2, where TGA is not a stop codon:
>>> translate(coding_dna, table=2)
'VAIVMGRWKGAR*'
>>> translate(coding_dna, table=2, to_stop=True)
'VAIVMGRWKGAR'
In fact this example uses an alternative start codon valid under NCBI
table 2, GTG, which means this example is a complete valid CDS which
when translated should really start with methionine (not valine):
>>> translate(coding_dna, table=2, cds=True)
'MAIVMGRWKGAR'
Note that if the sequence has no in-frame stop codon, then the to_stop
argument has no effect:
>>> coding_dna2 = "GTGGCCATTGTAATGGGCCGC"
>>> translate(coding_dna2)
'VAIVMGR'
>>> translate(coding_dna2, to_stop=True)
'VAIVMGR'
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.
It will however translate either DNA or RNA.
NOTE - Since version 1.71 Biopython contains codon tables with 'ambiguous
stop codons'. These are stop codons with unambiguous sequence but which
have a context dependent coding as STOP or as amino acid. With these tables
'to_stop' must be False (otherwise a ValueError is raised). The dual
coding codons will always be translated as amino acid, except for
'cds=True', where the last codon will be translated as STOP.
>>> coding_dna3 = "ATGGCACGGAAGTGA"
>>> translate(coding_dna3)
'MARK*'
>>> translate(coding_dna3, table=27) # Table 27: TGA -> STOP or W
'MARKW'
It will however raise a BiopythonWarning (not shown).
>>> translate(coding_dna3, table=27, cds=True)
'MARK'
>>> translate(coding_dna3, table=27, to_stop=True)
Traceback (most recent call last):
...
ValueError: You cannot use 'to_stop=True' with this table ...
"""
if isinstance(sequence, Seq):
return sequence.translate(table, stop_symbol, to_stop, cds)
elif isinstance(sequence, MutableSeq):
# Return a Seq object
return sequence.toseq().translate(table, stop_symbol, to_stop, cds)
else:
# Assume its a string, return a string
try:
codon_table = CodonTable.ambiguous_generic_by_id[int(table)]
except ValueError:
codon_table = CodonTable.ambiguous_generic_by_name[table]
except (AttributeError, TypeError):
if isinstance(table, CodonTable.CodonTable):
codon_table = table
else:
raise ValueError("Bad table argument")
return _translate_str(sequence, codon_table, stop_symbol, to_stop, cds, gap=gap)
def reverse_complement(sequence):
"""Return the reverse complement sequence of a nucleotide string.
If given a string, returns a new string object.
Given a Seq or a MutableSeq, returns a new Seq object with the same
alphabet.
Supports unambiguous and ambiguous nucleotide sequences.
e.g.
>>> reverse_complement("ACTG-NH")
'DN-CAGT'
"""
return complement(sequence)[::-1]
def complement(sequence):
"""Return the complement sequence of a nucleotide string.
If given a string, returns a new string object.
Given a Seq or a MutableSeq, returns a new Seq object with the same
alphabet.
Supports unambiguous and ambiguous nucleotide sequences.
e.g.
>>> complement("ACTG-NH")
'TGAC-ND'
"""
if isinstance(sequence, Seq):
# Return a Seq
return sequence.complement()
elif isinstance(sequence, MutableSeq):
# Return a Seq
# Don't use the MutableSeq reverse_complement method as it is
# 'in place'.
return sequence.toseq().complement()
# Assume its a string.
# In order to avoid some code duplication, the old code would turn the
# string into a Seq, use the reverse_complement method, and convert back
# to a string.
# This worked, but is over five times slower on short sequences!
if ("U" in sequence or "u" in sequence) and ("T" in sequence or "t" in sequence):
raise ValueError("Mixed RNA/DNA found")
elif "U" in sequence or "u" in sequence:
ttable = _rna_complement_table
else:
ttable = _dna_complement_table
return sequence.translate(ttable)
def _test():
"""Run the Bio.Seq module's doctests (PRIVATE)."""
print("Running doctests...")
import doctest
doctest.testmod(optionflags=doctest.IGNORE_EXCEPTION_DETAIL)
print("Done")
if __name__ == "__main__":
_test()
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