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Returns 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")(more...)

        def reverse_complement(sequence):
    """Returns 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'
    """
    if isinstance(sequence, Seq):
        #Return a Seq
        return sequence.reverse_complement()
    elif isinstance(sequence, MutableSeq):
        #Return a Seq
        #Don't use the MutableSeq reverse_complement method as it is 'in place'.
        return sequence.toseq().reverse_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)[::-1]
        


src/b/i/biopython-HEAD/Bio/SeqUtils/__init__.py   biopython(Download)
 
    """
    from Bio.Seq import reverse_complement, translate
    anti = reverse_complement(seq)
    comp = anti[::-1]

src/b/i/biopython-1.63/Scripts/xbbtools/xbb_translations.py   biopython(Download)
 
 
from Bio.Seq import reverse_complement, translate
from Bio.SeqUtils import GC
 
    def complement(self, seq):
        #TODO - use Seq methods instead of this hack:?
        return reverse_complement(seq)[::-1]
 
    def reverse(self, seq):
        return seq[::-1]
 
    def antiparallel(self, seq):
        return reverse_complement(seq)

src/b/i/biopython-HEAD/Scripts/xbbtools/xbb_translations.py   biopython(Download)
 
 
from Bio.Seq import reverse_complement, translate
from Bio.SeqUtils import GC
 
    def complement(self, seq):
        #TODO - use Seq methods instead of this hack:?
        return reverse_complement(seq)[::-1]
 
    def reverse(self, seq):
        return seq[::-1]
 
    def antiparallel(self, seq):
        return reverse_complement(seq)

src/b/i/biopython-1.63/Bio/SeqUtils/__init__.py   biopython(Download)
 
    """
    from Bio.Seq import reverse_complement, translate
    anti = reverse_complement(seq)
    comp = anti[::-1]

src/m/i/misc-genomics-tools-HEAD/mauve_xmfa_indexer/SeqUtils.py   misc-genomics-tools(Download)
from Bio.Seq import Seq, reverse_complement, translate
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
from Bio.Data import CodonTable
from Bio.Alphabet import IUPAC
        if int(strand) == -1:
            # we might have unicode here hence the cast
            seq = reverse_complement(str(seq))
        elif int(strand) == 1:
            pass
        if int(strand) == -1:
            # we might have unicode here hence the cast
            seq = reverse_complement(str(seq))
        elif int(strand) == 1:
            pass
 
    if strand < 0:
        ref_substr = reverse_complement(ref_substr)
        cns_substr = reverse_complement(cns_substr)
 

src/p/y/python-dna-0.1.2/pydna/utils.py   python-dna(Download)
    '''
 
    from Bio.Seq import reverse_complement
    from Bio.SeqRecord import SeqRecord
    import itertools
        # force circular comparison of all given sequences
        for s1, s2 in itertools.combinations(args_string_list, 2):
            if not ( s1 in s2+s2 or reverse_complement(s1) in s2+s2):
                same = False
    elif topology == "linear":
        # force linear comparison of all given sequences
        for s1,s2 in itertools.combinations(args_string_list, 2):
            if not ( s1==s2 or s1==reverse_complement(s2) ):
    import itertools
    import copy
    from Bio.Seq import reverse_complement
    from Bio.Seq import Seq
    from Bio.SeqRecord import SeqRecord
        a    = str(sequence).lower()
        a_rc = str(reverse_complement(sequence)).lower()
        sequence_rc = reverse_complement(sequence)
        double_sequence = a+a
 

src/p/y/pydna-0.6.1/pydna/utils.py   pydna(Download)
    '''
 
    from Bio.Seq import reverse_complement
    from Bio.SeqRecord import SeqRecord
    import itertools
        # force circular comparison of all given sequences
        for s1, s2 in itertools.combinations(args_string_list, 2):
            if not ( s1 in s2+s2 or reverse_complement(s1) in s2+s2):
                same = False
    elif topology == "linear":
        # force linear comparison of all given sequences
        for s1,s2 in itertools.combinations(args_string_list, 2):
            if not ( s1==s2 or s1==reverse_complement(s2) ):
    '''
    import re
    from Bio.Seq import reverse_complement as rc
    target_length    = len(target_sr)
    target_string    = str(target_sr.seq).upper()
 
    trgt_string = target_string
    trgt_string_rc = rc(trgt_string)
 
    for feature in [f for f in source_sr.features if len(f)>limit]:

src/b/i/biopython-1.63/Bio/SeqFeature.py   biopython(Download)
from __future__ import print_function
 
from Bio.Seq import MutableSeq, reverse_complement
 
 
            except AttributeError:
                assert isinstance(f_seq, str)
                f_seq = reverse_complement(f_seq)
        return f_seq
 

src/b/i/biopython-HEAD/Bio/SeqFeature.py   biopython(Download)
from __future__ import print_function
 
from Bio.Seq import MutableSeq, reverse_complement
 
 
            except AttributeError:
                assert isinstance(f_seq, str)
                f_seq = reverse_complement(f_seq)
        return f_seq
 

src/b/i/biopython-1.63/Scripts/xbbtools/xbb_search.py   biopython(Download)
 
from Bio.Data.IUPACData import ambiguous_dna_values
from Bio.Seq import reverse_complement
 
 
    def do_search(self, other_strand=0):
        pattern = self.get_pattern()
        if other_strand:
            pattern = reverse_complement(pattern)
        self.SetPattern(pattern)

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