def __init__(self, sequence, complement_in=b"ACGT", complement_out=b"TGCA", letters="ACGT"): """.. rubric:: Constructor A sequence is just a string stored in the :attr:`sequence` attribute. It has properties related to the type of alphabet authorised. :param str sequence: May be a string of a Fasta File, in which case only the first sequence is used. :param complement_in: :param complement_out: :param letters: authorise letters. Used in :meth:`check` only. .. todo:: use counter only once as a property """ if sequence.endswith(".fa") or sequence.endswith(".fasta"): fasta = FastA(sequence) sequence = fasta.next().sequence.upper() else: # assume correct string sequence pass self._data = sequence try: self._translate = string.maketrans(complement_in, complement_out) except: self._translate = bytes.maketrans(complement_in, complement_out) self._letters = letters
def __init__(self, sequence, complement_in=b"ACGT", complement_out=b"TGCA", letters="ACGT"): """.. rubric:: Constructor A sequence is just a string stored in the :attr:`sequence` attribute. It has properties related to the type of alphabet authorised. :param str sequence: May be a string of a Fasta File, in which case only the first sequence is used. :param complement_in: :param complement_out: :param letters: authorise letters. Used in :meth:`check` only. .. todo:: use counter only once as a property """ if sequence.endswith(".fa") or sequence.endswith(".fasta"): fasta = FastA(sequence) sequence = fasta.next().sequence.upper() else: # assume correct string sequence pass self._data = sequence try: self._translate = string.maketrans(complement_in, complement_out) except: self._translate = bytes.maketrans(complement_in, complement_out) self._letters = letters
class Sequence(object): """Abstract base classe for other specialised sequences such as DNA. Sequenced is the base class for other classes such as :class:`DNA` and :class:`RNA`. :: from sequana import Sequence s = Sequence("ACGT") s.stats() s.get_complement() .. note:: You may use a Fasta file as input (see constructor) """ def __init__(self, sequence, complement_in=b"ACGT", complement_out=b"TGCA", letters="ACGT"): """.. rubric:: Constructor A sequence is just a string stored in the :attr:`sequence` attribute. It has properties related to the type of alphabet authorised. :param str sequence: May be a string of a Fasta File, in which case only the first sequence is used. :param complement_in: :param complement_out: :param letters: authorise letters. Used in :meth:`check` only. .. todo:: use counter only once as a property """ if sequence.endswith(".fa") or sequence.endswith(".fasta"): self.fasta = FastA(sequence) sequence = self.fasta.next().sequence.upper() else: # assume correct string sequence pass self._data = sequence try: self._translate = string.maketrans(complement_in, complement_out) except: self._translate = bytes.maketrans(complement_in, complement_out) self._letters = letters def __iter__(self): return self def __next__(self): self._data = self.fasta.next().sequence.upper() return self._data def _get_sequence(self): return self._data sequence = property(_get_sequence) def get_complement(self): """Return complement """ return self._data.translate(self._translate) def get_reverse_complement(self): """Return reverse complement """ return self.get_complement()[::-1] def get_reverse(self): """Return reverse sequence""" return self._data[::-1] def complement(self): """Alias to :meth:`get_complement`""" self._data = self.get_complement() def reverse(self): """Alias to :meth:`get_reverse`""" self._data = self.get_reverse() def reverse_complement(self): """Alias to get_reverse_complement""" self._data = self.get_reverse_complement() def check(self): """Check that all letters are valid""" counter = Counter(self._data).keys() for key in counter: if key not in self._letters: raise ValueError( "Found unexpected letter in the sequence (%s)" % key) def __len__(self): return len(self._data) def gc_content(self): """Return mean GC content""" c = Counter(self._data) ratio = (c['G'] + c['C']) / len(self.sequence) return ratio def stats(self): """Return basic stats about the number of letters""" from collections import Counter return Counter(self.sequence) def get_occurences(self, pattern, overlap=False): """Return position of the input pattern in the sequence :: >>> from sequana import Sequence >>> s = Sequence('ACGTTTTACGT') >>> s.get_occurences("ACGT") [0, 7] """ if overlap is False: res = [m.start() for m in re.finditer(pattern, self.sequence)] elif overlap is True: res = [ m.start() for m in re.finditer('(?=%s)' % pattern, self.sequence) ] return res