Package Alphabet

Returns a common but often generic base alphabet object (PRIVATE).

This throws away any AlphabetEncoder information, e.g. Gapped alphabets.

Note that DNA+RNA -> Nucleotide, and Nucleotide+Protein-> generic single
letter.  These DO NOT raise an exception!

Returns a common but often generic alphabet object (PRIVATE).

>>> from Bio.Alphabet import IUPAC
>>> _consensus_alphabet([IUPAC.extended_protein, IUPAC.protein])
ExtendedIUPACProtein()
>>> _consensus_alphabet([generic_protein, IUPAC.protein])
ProteinAlphabet()

Note that DNA+RNA -> Nucleotide, and Nucleotide+Protein-> generic single
letter.  These DO NOT raise an exception!

>>> _consensus_alphabet([generic_dna, generic_nucleotide])
NucleotideAlphabet()
>>> _consensus_alphabet([generic_dna, generic_rna])
NucleotideAlphabet()
>>> _consensus_alphabet([generic_dna, generic_protein])
SingleLetterAlphabet()
>>> _consensus_alphabet([single_letter_alphabet, generic_protein])
SingleLetterAlphabet()

This is aware of Gapped and HasStopCodon and new letters added by
other AlphabetEncoders.  This WILL raise an exception if more than
one gap character or stop symbol is present.

>>> from Bio.Alphabet import IUPAC
>>> _consensus_alphabet([Gapped(IUPAC.extended_protein), HasStopCodon(IUPAC.protein)])
HasStopCodon(Gapped(ExtendedIUPACProtein(), '-'), '*')
>>> _consensus_alphabet([Gapped(IUPAC.protein, "-"), Gapped(IUPAC.protein, "=")])
Traceback (most recent call last):
    ...
ValueError: More than one gap character present
>>> _consensus_alphabet([HasStopCodon(IUPAC.protein, "*"), HasStopCodon(IUPAC.protein, "+")])
Traceback (most recent call last):
    ...
ValueError: More than one stop symbol present

Returns True except for DNA+RNA or Nucleotide+Protein (PRIVATE).

>>> _check_type_compatible([generic_dna, generic_nucleotide])
True
>>> _check_type_compatible([generic_dna, generic_rna])
False
>>> _check_type_compatible([generic_dna, generic_protein])
False
>>> _check_type_compatible([single_letter_alphabet, generic_protein])
True

This relies on the Alphabet subclassing hierarchy.  It does not
check things like gap characters or stop symbols.

Check all letters in sequence are in the alphabet (PRIVATE).

>>> from Bio.Seq import Seq
>>> from Bio.Alphabet import IUPAC
>>> my_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
...              IUPAC.protein)
>>> _verify_alphabet(my_seq)
True

This example has an X, which is not in the IUPAC protein alphabet
(you should be using the IUPAC extended protein alphabet):

>>> bad_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVFX",
...                IUPAC.protein)
>>> _verify_alphabet(bad_seq)
False

This replaces Bio.utils.verify_alphabet() since we are deprecating
that. Potentially this could be added to the Alphabet object, and
I would like it to be an option when creating a Seq object... but
that might slow things down.