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Uppercase IUPAC ambiguous DNA.

src/b/i/biopython-1.63/Bio/Nexus/Nexus.py   biopython(Download)
            self.datatype = options['datatype'].lower()
            if self.datatype == 'dna' or self.datatype == 'nucleotide':
                self.alphabet = IUPAC.IUPACAmbiguousDNA() # fresh instance!
                self.ambiguous_values = IUPACData.ambiguous_dna_values.copy()
                self.unambiguous_letters = IUPACData.unambiguous_dna_letters
            elif self.datatype == 'rna':
                self.alphabet = IUPAC.IUPACAmbiguousDNA() # fresh instance!

src/b/i/biopython-HEAD/Bio/Nexus/Nexus.py   biopython(Download)
            self.datatype = options['datatype'].lower()
            if self.datatype == 'dna' or self.datatype == 'nucleotide':
                self.alphabet = IUPAC.IUPACAmbiguousDNA() # fresh instance!
                self.ambiguous_values = IUPACData.ambiguous_dna_values.copy()
                self.unambiguous_letters = IUPACData.unambiguous_dna_letters
            elif self.datatype == 'rna':
                self.alphabet = IUPAC.IUPACAmbiguousDNA() # fresh instance!

src/p/y/python-dna-0.1.2/pydna/dsdna.py   python-dna(Download)
from Bio                    import Alphabet
from Bio                    import SeqIO
from Bio.Alphabet.IUPAC     import IUPACAmbiguousDNA
from Bio.Seq                import Seq
from Bio.Seq                import _maketrans
        handle = StringIO.StringIO(rawseq)
        try:
            parsed = SeqIO.read(handle, "embl", alphabet=IUPACAmbiguousDNA())
            original_format = "embl"
            if "circular" in rawseq.splitlines()[0]:
                circular = True
        except ValueError:
            handle.seek(0)
            try:
                parsed = SeqIO.read(handle, "genbank", alphabet=IUPACAmbiguousDNA())
                handle.seek(0)
                try:
                    parsed = SeqIO.read(handle, "fasta", alphabet=IUPACAmbiguousDNA())
                    original_format = "fasta"
                    if "circular" in rawseq.splitlines()[0]:

src/p/y/python-dna-0.1.2/scripts/pydna_helper/pydna_helper.py   python-dna(Download)
# coding: utf-8
from Bio import SeqIO
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
 
global new_primer
global old_primer_dict
 
new_primer = list(SeqIO.parse("/home/bjorn/Dropbox/wikidata/PrimersToBuy.wiki", "fasta", IUPACAmbiguousDNA()))
primer     = list(SeqIO.parse("/home/bjorn/Dropbox/wikidata/Primers.wiki", "fasta" ,IUPACAmbiguousDNA()))
 

src/p/y/pydna-0.6.1/pydna/dsdna.py   pydna(Download)
from Bio                    import Alphabet
from Bio                    import SeqIO
from Bio.Alphabet.IUPAC     import IUPACAmbiguousDNA
from Bio.Seq                import Seq
from Bio.Seq                import _maketrans
 
        try:
            parsed = SeqIO.read(handle, "embl", alphabet=IUPACAmbiguousDNA())
            original_format = "embl"
            if "circular" in rawseq.splitlines()[0]:
                circular = True
        except ValueError:
            handle.seek(0)
            try:
                parsed = SeqIO.read(handle, "genbank", alphabet=IUPACAmbiguousDNA())
                handle.seek(0)
                try:
                    parsed = SeqIO.read(handle, "fasta", alphabet=IUPACAmbiguousDNA())
                    original_format = "fasta"
                    if "circular" in rawseq.splitlines()[0]:

src/p/y/python-dna-0.1.2/scripts/pydna_helper/load_my_primers.py   python-dna(Download)
# coding: utf-8
from Bio import SeqIO
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
 
from pydna import parse

src/p/y/python-dna-0.1.2/pydna/download.py   python-dna(Download)
from Bio                    import SeqIO
from Bio                    import Entrez
from Bio.Alphabet.IUPAC     import IUPACAmbiguousDNA
from Bio.GenBank            import RecordParser
from Bio.SeqUtils.CheckSum  import seguid

src/p/y/pydna-0.6.1/pydna/download.py   pydna(Download)
from Bio                    import SeqIO
from Bio                    import Entrez
from Bio.Alphabet.IUPAC     import IUPACAmbiguousDNA
from Bio.GenBank            import RecordParser
from Bio.SeqUtils.CheckSum  import seguid

src/m/g/mgtaxa-HEAD/test/py/test_Bio_GenBank.py   mgtaxa(Download)
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature,FeatureLocation
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
 
#gbFile = pjoin(options.testDataDir,"iofilt.test.gz")

src/b/i/biopython-HEAD/Tests/test_seq.py   biopython(Download)
            Seq.Seq("".join(sorted(ambiguous_dna_values)), Alphabet.generic_dna),
            Seq.Seq("".join(sorted(ambiguous_rna_values)).replace("X", ""), IUPAC.IUPACAmbiguousRNA()),
            Seq.Seq("".join(sorted(ambiguous_dna_values)).replace("X", ""), IUPAC.IUPACAmbiguousDNA()),
            Seq.Seq("AWGAARCKG")]:  # Note no U or T
        print("%s -> %s" \

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