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Standard nucleotide and protein alphabets defined by IUPAC.

src/s/e/seqmagick-0.5.0/seqmagick/transform.py   seqmagick(Download)
 
from Bio import SeqIO
from Bio.Alphabet import IUPAC
from Bio.Data import CodonTable
from Bio.Seq import Seq

src/w/l/wLib-1.1.0/external/Motif/_Motif.py   wLib(Download)
from Bio.Seq import Seq
from Bio.SubsMat import FreqTable
from Bio.Alphabet import IUPAC
import math,random
 

src/c/g/cgat-HEAD/scripts/fasta2distances.py   cgat(Download)
 
import CGAT.FastaIterator as FastaIterator
import Bio.Alphabet.IUPAC
 
# -------------------------------------------------------------------------

src/c/g/cgat-HEAD/scripts/analyze_sequences.py   cgat(Download)
 
import CGAT.FastaIterator as FastaIterator
import Bio.Alphabet.IUPAC
 
 

src/c/g/cgat-HEAD/obsolete/fasta2properties.py   cgat(Download)
from CGAT.SequenceProperties import *
import CGAT.FastaIterator as FastaIterator
import Bio.Alphabet.IUPAC
 
##---------------------------------------------------------------------------------------------

src/c/g/cgat-HEAD/CGAT/SequenceProperties.py   cgat(Download)
from CGAT import IOTools as IOTools
 
import Bio.Alphabet.IUPAC
 
 

src/b/i/biopython---popgen-HEAD/src/PopGen/Gio/HaplotypesGenerator.py   biopython---popgen(Download)
 
        if alphabet is None:
            from Bio.Alphabet import IUPAC
            self.alphabet = IUPAC.IUPACUnambiguousDNA()
 

src/s/e/seqmagick-HEAD/seqmagick/transform.py   seqmagick(Download)
 
from Bio import SeqIO
from Bio.Alphabet import IUPAC
from Bio.Data import CodonTable
from Bio.Seq import Seq

src/c/l/clusterDbAnalysis-HEAD/scripts/kbaseGenomeToGenbank.py   clusterDbAnalysis(Download)
# These are from Biopython
from Bio import SeqIO
from Bio.Alphabet import IUPAC
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio.SeqRecord import SeqRecord

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
 
    from Bio import Translate
    from Bio.Alphabet import IUPAC
    from Bio.Seq import Seq
    bacteria_translator = Translate.ambiguous_dna_by_id[11]

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