Did I find the right examples for you? yes no      Crawl my project      Python Jobs

All Samples(69)  |  Call(63)  |  Derive(0)  |  Import(6)

src/b/i/biopython-1.63/Bio/Seq.py   biopython(Download)
        ValueError: Proteins do not have complements!
        """
        base = Alphabet._get_base_alphabet(self.alphabet)
        if isinstance(base, Alphabet.ProteinAlphabet):
            raise ValueError("Proteins do not have complements!")
        ValueError: Proteins cannot be transcribed!
        """
        base = Alphabet._get_base_alphabet(self.alphabet)
        if isinstance(base, Alphabet.ProteinAlphabet):
            raise ValueError("Proteins cannot be transcribed!")
        ValueError: Proteins cannot be back transcribed!
        """
        base = Alphabet._get_base_alphabet(self.alphabet)
        if isinstance(base, Alphabet.ProteinAlphabet):
            raise ValueError("Proteins cannot be back transcribed!")
                             + "the python string object's translate method. "
                             + "Use str(my_seq).translate(...) instead.")
        if isinstance(Alphabet._get_base_alphabet(self.alphabet),
                      Alphabet.ProteinAlphabet):
            raise ValueError("Proteins cannot be translated!")
            self._character = character
        else:
            base = Alphabet._get_base_alphabet(alphabet)
            #TODO? Check the case of the letters in the alphabet?
            #We may have to use "n" instead of "N" etc.

src/b/i/biopython-HEAD/Bio/Seq.py   biopython(Download)
        ValueError: Proteins do not have complements!
        """
        base = Alphabet._get_base_alphabet(self.alphabet)
        if isinstance(base, Alphabet.ProteinAlphabet):
            raise ValueError("Proteins do not have complements!")
        ValueError: Proteins cannot be transcribed!
        """
        base = Alphabet._get_base_alphabet(self.alphabet)
        if isinstance(base, Alphabet.ProteinAlphabet):
            raise ValueError("Proteins cannot be transcribed!")
        ValueError: Proteins cannot be back transcribed!
        """
        base = Alphabet._get_base_alphabet(self.alphabet)
        if isinstance(base, Alphabet.ProteinAlphabet):
            raise ValueError("Proteins cannot be back transcribed!")
                             + "the python string object's translate method. "
                             + "Use str(my_seq).translate(...) instead.")
        if isinstance(Alphabet._get_base_alphabet(self.alphabet),
                      Alphabet.ProteinAlphabet):
            raise ValueError("Proteins cannot be translated!")
            self._character = character
        else:
            base = Alphabet._get_base_alphabet(alphabet)
            #TODO? Check the case of the letters in the alphabet?
            #We may have to use "n" instead of "N" etc.

src/b/i/biopython-1.63/Bio/Align/AlignInfo.py   biopython(Download)
        """
        #Start with the (un-gapped version of) the alignment alphabet
        a = Alphabet._get_base_alphabet(self.alignment._alphabet)
 
        #Now check its compatible with all the rest of the sequences
        for record in self.alignment:
            #Get the (un-gapped version of) the sequence's alphabet
            alt = Alphabet._get_base_alphabet(record.seq.alphabet)
        if not e_freq_table:
            #TODO - What about ambiguous alphabets?
            base_alpha = Alphabet._get_base_alphabet(self.alignment._alphabet)
            if isinstance(base_alpha, Alphabet.ProteinAlphabet):
                random_expected = Protein20Random

src/b/i/biopython-HEAD/Bio/Align/AlignInfo.py   biopython(Download)
        """
        #Start with the (un-gapped version of) the alignment alphabet
        a = Alphabet._get_base_alphabet(self.alignment._alphabet)
 
        #Now check its compatible with all the rest of the sequences
        for record in self.alignment:
            #Get the (un-gapped version of) the sequence's alphabet
            alt = Alphabet._get_base_alphabet(record.seq.alphabet)
        if not e_freq_table:
            #TODO - What about ambiguous alphabets?
            base_alpha = Alphabet._get_base_alphabet(self.alignment._alphabet)
            if isinstance(base_alpha, Alphabet.ProteinAlphabet):
                random_expected = Protein20Random

src/b/i/biopython-1.63/Bio/AlignIO/__init__.py   biopython(Download)
from Bio.Align import MultipleSeqAlignment
from Bio.Align.Generic import Alignment
from Bio.Alphabet import Alphabet, AlphabetEncoder, _get_base_alphabet
from Bio.File import as_handle
 
    given_base_class = _get_base_alphabet(alphabet).__class__
    for align in alignment_iterator:
        if not isinstance(_get_base_alphabet(align._alphabet),
                          given_base_class):
            raise ValueError("Specified alphabet %s clashes with "
                             "that determined from the file, %s"
                             % (repr(alphabet), repr(align._alphabet)))
        for record in align:
            if not isinstance(_get_base_alphabet(record.seq.alphabet),

src/b/i/biopython-HEAD/Bio/AlignIO/__init__.py   biopython(Download)
from Bio.Align import MultipleSeqAlignment
from Bio.Align.Generic import Alignment
from Bio.Alphabet import Alphabet, AlphabetEncoder, _get_base_alphabet
from Bio.File import as_handle
 
    given_base_class = _get_base_alphabet(alphabet).__class__
    for align in alignment_iterator:
        if not isinstance(_get_base_alphabet(align._alphabet),
                          given_base_class):
            raise ValueError("Specified alphabet %s clashes with "
                             "that determined from the file, %s"
                             % (repr(alphabet), repr(align._alphabet)))
        for record in align:
            if not isinstance(_get_base_alphabet(record.seq.alphabet),

src/b/i/biopython-HEAD/Bio/SeqUtils/__init__.py   biopython(Download)
    tmp_type = ''
    if isinstance(seq, Seq) or isinstance(seq, MutableSeq):
        base_alphabet = Alphabet._get_base_alphabet(seq.alphabet)
        if isinstance(base_alphabet, Alphabet.DNAAlphabet):
            tmp_type = 'DNA'

src/b/i/biopython-1.63/Bio/SeqIO/__init__.py   biopython(Download)
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment
from Bio.Alphabet import Alphabet, AlphabetEncoder, _get_base_alphabet
 
from . import AbiIO
    given_base_class = _get_base_alphabet(alphabet).__class__
    for record in record_iterator:
        if isinstance(_get_base_alphabet(record.seq.alphabet),
                      given_base_class):
            record.seq.alphabet = alphabet

src/b/i/biopython-HEAD/Bio/SeqIO/__init__.py   biopython(Download)
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment
from Bio.Alphabet import Alphabet, AlphabetEncoder, _get_base_alphabet
 
from . import AbiIO
    given_base_class = _get_base_alphabet(alphabet).__class__
    for record in record_iterator:
        if isinstance(_get_base_alphabet(record.seq.alphabet),
                      given_base_class):
            record.seq.alphabet = alphabet

src/b/i/biopython-1.63/Bio/SeqIO/SffIO.py   biopython(Download)
 
    """
    if isinstance(Alphabet._get_base_alphabet(alphabet),
                  Alphabet.ProteinAlphabet):
        raise ValueError("Invalid alphabet, SFF files do not hold proteins.")
    if isinstance(Alphabet._get_base_alphabet(alphabet),

  1 | 2 | 3  Next