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Returns the SEGUID (string) for a sequence (string or Seq object).

Given a nucleotide or amino-acid secuence (or any string),
returns the SEGUID string (A SEquence Globally Unique IDentifier).
seq type = str.
For more information about SEGUID, see:
http://bioinformatics.anl.gov/seguid/
DOI: 10.1002/pmic.200600032 

        def seguid(seq):
    """Returns the SEGUID (string) for a sequence (string or Seq object).

    Given a nucleotide or amino-acid secuence (or any string),
    returns the SEGUID string (A SEquence Globally Unique IDentifier).
    seq type = str.
    For more information about SEGUID, see:
    http://bioinformatics.anl.gov/seguid/
    DOI: 10.1002/pmic.200600032 """
    import hashlib
    import base64
    m = hashlib.sha1()
    try:
        #Assume it's a Seq object
        seq = str(seq)
    except AttributeError:
        #Assume it's a string
        pass
    m.update(_as_bytes(seq.upper()))
    try:
        #For Python 3+
        return base64.encodebytes(m.digest()).decode().replace("\n", "").rstrip("=")
    except AttributeError:
        pass
    # For all other Pythons
    return base64.b64encode(m.digest()).rstrip("=")
        


src/p/y/python-dna-0.1.2/pydna/assembly.py   python-dna(Download)
from Bio.Seq                 import Seq
from Bio.Seq                 import reverse_complement as rc
from Bio.SeqUtils.CheckSum   import seguid
 
from findsubstrings_suffix_arrays_python        import common_sub_strings
            incoming = [(n, keynode) for n in G.predecessors(keynode) if n not in circular_path]
            outgoing = [(keynode, n) for n in G.successors(keynode) if n not in circular_path]
            new_node = seguid(sm.seq)
            G.add_node(new_node, sek=sm)
            G.add_edges_from( [(p[0], new_node, {'sek' : G[p[0]][p[1]][0]['sek'] }) for p in incoming] )
            incoming = [(n, keynode) for n in G.predecessors(keynode) if n not in circular_path]
            outgoing = [(keynode, n) for n in G.successors(keynode) if n not in circular_path]
            new_node = seguid(sm.seq)
            G.add_node(new_node, sek=sm)
            G.add_edges_from( [(p[0], new_node, {'sek' : G[p[0]][p[1]][0]['sek'] }) for p in incoming] )
            assert str(node_seq.seq).lower() == str(node_seq2.seq).lower()
            node_seq.features.extend(node_seq2.features)
            chksum = seguid(node_seq.seq)
            G.add_node(chksum, sek = node_seq)
 

src/p/y/python-dna-0.1.2/pydna/download.py   python-dna(Download)
from Bio.Alphabet.IUPAC     import IUPACAmbiguousDNA
from Bio.GenBank            import RecordParser
from Bio.SeqUtils.CheckSum  import seguid
 
from pydna.dsdna import read
        except urllib2.URLError:
            return False
        return seguid(result.seq) == "71B4PwSgBZ3htFjJXwHPxtUIPYE"
 
    def nucleotide(self, item):

src/p/y/pydna-0.6.1/pydna/utils.py   pydna(Download)
 
'''
from Bio.SeqUtils.CheckSum  import seguid
from itertools import tee, izip
from Bio.SeqFeature import SeqFeature
    '''
    from Bio.Seq import reverse_complement as rc
    return seguid( min( SmallestRotation(str(seq)), SmallestRotation(str(rc(seq)))))
 
if __name__ == "__main__":

src/p/y/pydna-0.6.1/pydna/download.py   pydna(Download)
from Bio.Alphabet.IUPAC     import IUPACAmbiguousDNA
from Bio.GenBank            import RecordParser
from Bio.SeqUtils.CheckSum  import seguid
 
from pydna.dsdna import read
        except urllib2.URLError:
            return False
        return seguid(result.seq) == "71B4PwSgBZ3htFjJXwHPxtUIPYE"
 
    def nucleotide(self, item, start=None, stop=None, strand="watson" ):

src/s/e/seqmagick-0.5.0/seqmagick/transform.py   seqmagick(Download)
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqUtils.CheckSum import seguid
 
# Characters to be treated as gaps
    checksum_sequences = collections.defaultdict(list)
    for record in records:
        checksum = seguid(record.seq)
        sequences = checksum_sequences[checksum]
        if not sequences:

src/s/e/seqmagick-HEAD/seqmagick/transform.py   seqmagick(Download)
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqUtils.CheckSum import seguid
 
# Characters to be treated as gaps
    checksum_sequences = collections.defaultdict(list)
    for record in records:
        checksum = seguid(record.seq)
        sequences = checksum_sequences[checksum]
        if not sequences:

src/p/y/python-dna-0.1.2/scripts/pGUP1/pGUP1.py   python-dna(Download)
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqUtils.CheckSum import seguid
 
 

src/p/y/pydna-0.6.1/scripts/pGUP1/pGUP1.py   pydna(Download)
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.SeqUtils.CheckSum import seguid
 
 

src/p/y/python-dna-0.1.2/pydna/dsdna.py   python-dna(Download)
from Bio.SeqFeature         import SeqFeature
from Bio.SeqFeature         import FeatureLocation
from Bio.SeqUtils.CheckSum  import seguid
from Bio.GenBank            import RecordParser
from pydna.utils            import eq

src/p/y/python-dna-0.1.2/pydna/amplify.py   python-dna(Download)
 
from StringIO                       import StringIO
from Bio.SeqUtils.CheckSum          import seguid
from math                           import log10
from math                           import log

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