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**********************************************
Using the ``MolType`` and ``Sequence`` objects
**********************************************
.. authors Meg Pirrung
MolType
=======
``MolType`` provides services for resolving ambiguities, or providing the correct ambiguity for recoding. It also maintains the mappings between different kinds of alphabets, sequences and alignments.
One issue with ``MolType``'s is that they need to know about ``Sequence``, ``Alphabet``, and other objects, but, at the same time, those objects need to know about the ``MolType``. It is thus essential that the connection between these other types and the ``MolType`` can be made after the objects are created.
Setting up a ``MolType`` object with an RNA sequence
----------------------------------------------------
.. doctest::
>>> from cogent.core.moltype import MolType, IUPAC_RNA_chars,\
... IUPAC_RNA_ambiguities, RnaStandardPairs, RnaMW,\
... IUPAC_RNA_ambiguities_complements
>>> from cogent.core.sequence import NucleicAcidSequence
>>> testrnaseq = 'ACGUACGUACGUACGU'
>>> RnaMolType = MolType(
... Sequence = NucleicAcidSequence(testrnaseq),
... motifset = IUPAC_RNA_chars,
... Ambiguities = IUPAC_RNA_ambiguities,
... label = "rna_with_lowercase",
... MWCalculator = RnaMW,
... Complements = IUPAC_RNA_ambiguities_complements,
... Pairs = RnaStandardPairs,
... add_lower=True,
... preserve_existing_moltypes=True,
... make_alphabet_group=True,
... )
Setting up a ``MolType`` object with a DNA sequence
---------------------------------------------------
.. doctest::
>>> from cogent.core.moltype import MolType, IUPAC_DNA_chars,\
... IUPAC_DNA_ambiguities, DnaMW, IUPAC_DNA_ambiguities_complements,\
... DnaStandardPairs
>>> testdnaseq = 'ACGTACGTACGUACGT'
>>> DnaMolType = MolType(
... Sequence = NucleicAcidSequence(testdnaseq),
... motifset = IUPAC_DNA_chars,
... Ambiguities = IUPAC_DNA_ambiguities,
... label = "dna_with_lowercase",
... MWCalculator = DnaMW,
... Complements = IUPAC_DNA_ambiguities_complements,
... Pairs = DnaStandardPairs,
... add_lower=True,
... preserve_existing_moltypes=True,
... make_alphabet_group=True,
... )
Setting up a ``MolType`` object with a protein sequence
-------------------------------------------------------
.. doctest::
>>> from cogent.core.moltype import MolType, IUPAC_PROTEIN_chars,\
... IUPAC_PROTEIN_ambiguities, ProteinMW
>>> from cogent.core.sequence import ProteinSequence, ModelProteinSequence
>>> protstr = 'TEST'
>>> ProteinMolType = MolType(
... Sequence = ProteinSequence(protstr),
... motifset = IUPAC_PROTEIN_chars,
... Ambiguities = IUPAC_PROTEIN_ambiguities,
... MWCalculator = ProteinMW,
... make_alphabet_group=True,
... ModelSeq = ModelProteinSequence,
... label = "protein")
>>> protseq = ProteinMolType.Sequence
Verify sequences
----------------
.. doctest::
>>> rnastr = 'ACGUACGUACGUACGU'
>>> dnastr = 'ACGTACGTACGTACGT'
>>> RnaMolType.isValid(rnastr)
True
>>> RnaMolType.isValid(dnastr)
False
>>> RnaMolType.isValid(NucleicAcidSequence(dnastr).toRna())
True
``Sequence``
============
The ``Sequence`` object contains classes that represent biological sequence data. These provide generic biological sequence manipulation functions, plus functions that are critical for the ``evolve`` module calculations.
.. warning:: Do not import sequence classes directly! It is expected that you will access them through ``MolType`` objects. The most common molecular types ``DNA``, ``RNA``, ``PROTEIN`` are provided as top level imports in cogent (e.g. ``cogent.DNA``). Sequence classes depend on information from the ``MolType`` that is **only** available after ``MolType`` has been imported. Sequences are intended to be immutable. This is not enforced by the code for performance reasons, but don't alter the ``MolType`` or the sequence data after creation.
More detailed usage of sequence objects can be found in :ref:`dna-rna-seqs`.
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