nucleic module

class nucleic.DNA(sequence, metadata=None, positional_metadata=None, lowercase=False, validate=True)[source]

Bases: skbio.sequence._grammared_sequence.GrammaredSequence, skbio.sequence._nucleotide_mixin.NucleotideMixin

Deoxyribonucleic acid composed of the following nucleotide sequences:

String Residue Class
A Adenine Purine
C Cytosine Pyrimidine
G Guanine Purine
T Thymine Pyrimidine

Examples

>>> dna = DNA("A")
>>> dna.is_purine()
True
>>> dna.complement()
DNA("T")
>>> DNA("T").to("A")
Variant(ref=DNA("T"), alt=DNA("A"), context=DNA("T"))
is_purine() → bool[source]

Return if this sequence is a purine.

is_pyrimidine() → bool[source]

Return if this sequence is a pyrimdine.

to(other: Union[str, DNA]) → nucleic.Variant[source]

Create a variant allele.

class nucleic.Notation[source]

Bases: enum.Enum

An enumeration.

nucleic.Nt(seq: Union[str, nucleic.DNA]) → nucleic.DNA[source]

A single nucleotide of DNA.

Warning

Will be deprecated in v0.7.0. Use nucleic.DNA instead.

nucleic.Snv(ref: nucleic.DNA, alt: nucleic.DNA, context: Optional[nucleic.DNA] = None) → nucleic.Variant[source]

A single nucleotide variant of type Variant.

Warning

Will be deprecated in v0.7.0. Use nucleic.Variant instead.

class nucleic.SnvSpectrum(k: int = 3, notation: nucleic.Notation = <Notation.none: 0>)[source]

Bases: nucleic.util.DictMostCommonMixin, nucleic.util.DictNpArrayMixin, collections.OrderedDict

contexts() → numpy.ndarray[source]

Return all Variant key as a numpy.ndarray.

Warning

Will be deprecated in v0.7.0. Use nucleic.SnvSpectrum.weights.keys instead.

counts

Return all single nucleotide variants and their counts.

Warning

Will be deprecated in v0.7.0. Use nucleic.SnvSpectrum instead.

counts_as_array() → numpy.ndarray[source]

Return all counts as a numpy.ndarray.

Warning

Will be deprecated in v0.7.0. Use nucleic.SnvSpectrum.values() instead.

mass() → numpy.ndarray[source]

Return the discrete probability mass of this spectrum.

Raises:ValueError – if an observation is found with zero context weight.
snvs() → numpy.ndarray[source]

Return all Variant key as a numpy.ndarray.

Warning

Will be deprecated in v0.7.0. Use nucleic.SnvSpectrum.keys instead.

split_by_notation() → Tuple[nucleic.SnvSpectrum, nucleic.SnvSpectrum][source]

Split pyrimidine vs purine reference variants into seperate spectrum.

Raises:ValueError – if the notation of this spectrum is not Notation.none.
Returns:spectrum_pu – A SnvSpectrum holding purine reference variants. spectrum_py: A SnvSpectrum holding pyrimidine reference variants.

Note

  • TODO: Return a collection holding the two spectrum, like namedtuple.
weights_as_array() → numpy.ndarray[source]

Return all weights as a numpy.ndarray.

Warning

Will be deprecated in v0.7.0. Use nucleic.SnvSpectrum.weights.values instead.

nucleic.fetch_cosmic_signatures() → Dict[source]

Fetch the COSMIC published signatures from the following URL.

Returns:signatures – The probability masses of the COSMIC signatures.