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src/p/y/pytools-HEAD/SeqRecordLite.py   pytools(Download)
import copy
 
from Bio.Seq import Seq, UnknownSeq
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation
    def __init__(self, biopython_object=None):
 
        # first we define our underlying SeqRecord object
        if biopython_object == None:
            self._record = SeqRecord(seq=UnknownSeq(0,alphabet=NucleotideAlphabet()),id='',name='',description='')

src/b/i/biopython-1.63/Bio/GenBank/__init__.py   biopython(Download)
        from Bio import Alphabet
        from Bio.Alphabet import IUPAC
        from Bio.Seq import Seq, UnknownSeq
 
        #Try and append the version number to the accession for the full id
 
        if not sequence and self.__expected_size:
            self.data.seq = UnknownSeq(self._expected_size, seq_alphabet)
        else:
            self.data.seq = Seq(sequence, seq_alphabet)

src/b/i/biopython-HEAD/Bio/GenBank/__init__.py   biopython(Download)
        from Bio import Alphabet
        from Bio.Alphabet import IUPAC
        from Bio.Seq import Seq, UnknownSeq
 
        #Try and append the version number to the accession for the full id
 
        if not sequence and self.__expected_size:
            self.data.seq = UnknownSeq(self._expected_size, seq_alphabet)
        else:
            self.data.seq = Seq(sequence, seq_alphabet)

src/b/i/biopython-1.63/Bio/SeqIO/QualityIO.py   biopython(Download)
 
from Bio.Alphabet import single_letter_alphabet
from Bio.Seq import Seq, UnknownSeq
from Bio.SeqRecord import SeqRecord
from Bio.SeqIO.Interfaces import SequentialSequenceWriter
 
        #Return the record and then continue...
        record = SeqRecord(UnknownSeq(len(qualities), alphabet),
                           id=id, name=name, description=descr)
        #Dirty trick to speed up this line:

src/b/i/biopython-HEAD/Bio/SeqIO/QualityIO.py   biopython(Download)
 
from Bio.Alphabet import single_letter_alphabet
from Bio.Seq import Seq, UnknownSeq
from Bio.SeqRecord import SeqRecord
from Bio.SeqIO.Interfaces import SequentialSequenceWriter
 
        #Return the record and then continue...
        record = SeqRecord(UnknownSeq(len(qualities), alphabet),
                           id=id, name=name, description=descr)
        #Dirty trick to speed up this line:

src/b/i/biopython-1.63/BioSQL/BioSeq.py   biopython(Download)
 
from Bio import Alphabet
from Bio.Seq import Seq, UnknownSeq
from Bio.SeqRecord import SeqRecord, _RestrictedDict
from Bio import SeqFeature
        return DBSeq(primary_id, adaptor, alphabet, 0, int(length))
    else:
        return UnknownSeq(length, alphabet)
 
 

src/b/i/biopython-HEAD/BioSQL/BioSeq.py   biopython(Download)
 
from Bio import Alphabet
from Bio.Seq import Seq, UnknownSeq
from Bio.SeqRecord import SeqRecord, _RestrictedDict
from Bio import SeqFeature
        return DBSeq(primary_id, adaptor, alphabet, 0, int(length))
    else:
        return UnknownSeq(length, alphabet)
 
 

src/b/c/bcbb-HEAD/gff/BCBio/GFF/GFFParser.py   bcbb(Download)
    collections.defaultdict = _utils.defaultdict
 
from Bio.Seq import UnknownSeq
from Bio.SeqRecord import SeqRecord
from Bio import SeqFeature
        except KeyError:
            if self._create_missing:
                new_rec = SeqRecord(UnknownSeq(max_loc), info_dict['rec_id'])
                base[info_dict['rec_id']] = new_rec
                return new_rec, base

src/b/c/bcbio-gff-0.4/BCBio/GFF/GFFParser.py   bcbio-gff(Download)
    collections.defaultdict = _utils.defaultdict
 
from Bio.Seq import UnknownSeq
from Bio.SeqRecord import SeqRecord
from Bio import SeqFeature
        except KeyError:
            if self._create_missing:
                new_rec = SeqRecord(UnknownSeq(max_loc), info_dict['rec_id'])
                base[info_dict['rec_id']] = new_rec
                return new_rec, base

src/b/i/biopython-1.63/Tests/test_Seq_objs.py   biopython(Download)
from Bio.Alphabet.IUPAC import unambiguous_dna, ambiguous_dna, ambiguous_rna
from Bio.Data.IUPACData import ambiguous_dna_values, ambiguous_rna_values
from Bio.Seq import Seq, UnknownSeq, MutableSeq, translate
from Bio.Data.CodonTable import TranslationError, CodonTable
 
        Seq("A", generic_dna),
        Seq("A", generic_rna),
        UnknownSeq(1),
        UnknownSeq(1, character="n"),
        UnknownSeq(1, generic_rna),
        UnknownSeq(1, generic_rna, "n"),

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