Oligonucleotides: RNA
=====================

Nucleic Acid Sequences
**********************

OpenMS also supports the representation of RNA oligonucleotides using the :py:class:`~.NASequence` class:

.. code-block:: python
    :linenos:

    import pyopenms as oms

    oligo = oms.NASequence.fromString("AAUGCAAUGG")
    prefix = oligo.getPrefix(4)
    suffix = oligo.getSuffix(4)

    print(oligo)
    print(prefix)
    print(suffix)
    print()

    print("Oligo length", oligo.size())
    print("Total precursor mass", oligo.getMonoWeight())
    print(
        "y1+ ion mass of",
        str(prefix),
        ":",
        prefix.getMonoWeight(oms.NASequence.NASFragmentType.YIon, 1),
    )
    print()

    seq_formula = oligo.getFormula()
    print("RNA Oligo", oligo, "has molecular formula", seq_formula)
    print("=" * 35)
    print()

    isotopes = seq_formula.getIsotopeDistribution(oms.CoarseIsotopePatternGenerator(6))
    for iso in isotopes.getContainer():
        print("Isotope", iso.getMZ(), ":", iso.getIntensity())


Which will output

.. code-block:: output


    AAUGCAAUGG
    AAUG
    AUGG

    Oligo length 10
    Total precursor mass 3206.4885302061
    y1+ ion mass of AAUG : 1248.2298440331

    RNA Oligo AAUGCAAUGG has molecular formula C97H119N42O66P9
    ===================================

    Isotope 3206.4885302061 : 0.25567981600761414
    Isotope 3207.4918850439003 : 0.31783154606819153
    Isotope 3208.4952398817004 : 0.23069815337657928
    Isotope 3209.4985947195 : 0.12306403368711472
    Isotope 3210.5019495573 : 0.053163252770900726
    Isotope 3211.5053043951 : 0.01956319250166416



The :py:class:`~.NASequence` object also allows iterations directly in Python:

.. code-block:: python
    :linenos:

    oligo = oms.NASequence.fromString("AAUGCAAUGG")
    print(
        "The oligonucleotide", str(oligo), "consists of the following nucleotides:"
    )
    for ribo in oligo:
        print(ribo.getName())

Fragment Ions
~~~~~~~~~~~~~

Similarly to before for amino acid sequences, we can also generate internal fragment ions:

.. code-block:: python
    :linenos:

    oligo = oms.NASequence.fromString("AAUGCAAUGG")
    suffix = oligo.getSuffix(4)

    oligo.size()
    oligo.getMonoWeight()

    charge = 2
    mass = suffix.getMonoWeight(oms.NASequence.NASFragmentType.WIon, charge)
    w4_formula = suffix.getFormula(oms.NASequence.NASFragmentType.WIon, charge)
    mz = mass / charge

    print("=" * 35)
    print("RNA Oligo w4++ ion", suffix, "has mz", mz)
    print("RNA Oligo w4++ ion", suffix, "has molecular formula", w4_formula)

Modified Oligonucleotides
*************************

Modified nucleotides can also be represented by the :py:class:`~.Ribonucleotide` class and
are specified using a unique string identifier present in the
:py:class:`~.RibonucleotideDB` in square brackets. For example, :chem:`[m1A]` represents
1-methyl-adenosine. We can create a :py:class:`~.NASequence` object by parsing a modified
sequence as follows:

.. code-block:: python
    :linenos:

    oligo_mod = oms.NASequence.fromString("A[m1A][Gm]A")
    seq_formula = oligo_mod.getFormula()
    print(
        "RNA Oligo",
        oligo_mod,
        "has molecular formula",
        seq_formula,
        "and length",
        oligo_mod.size(),
    )
    print("=" * 35)

    oligo_list = [oligo_mod[i].getOrigin() for i in range(oligo_mod.size())]
    print(
        "RNA Oligo",
        oligo_mod.toString(),
        "has unmodified sequence",
        "".join(oligo_list),
    )

    r = oligo_mod[1]
    r.getName()
    r.getHTMLCode()
    r.getOrigin()

    for i in range(oligo_mod.size()):
        print(oligo_mod[i].isModified())


DNA, RNA and Protein
********************

We can also work with DNA and RNA sequences in combination with the BioPython
library (you can install BioPython with ``pip install biopython``):

.. code-block:: pseudocode
    :linenos:

    from Bio.Seq import Seq
    from Bio.Alphabet import IUPAC
    bsa = oms.FASTAEntry()
    bsa.sequence = 'ATGAAGTGGGTGACTTTTATTTCTCTTCTCCTTCTCTTCAGCTCTGCTTATTCCAGGGGTGTGTTTCGT'
    bsa.description = "BSA Bovine Albumin (partial sequence)"
    bsa.identifier = "BSA"

    entries = [bsa]

    f = oms.FASTAFile()
    f.store("example_dna.fasta", entries)

    coding_dna = Seq(bsa.sequence, IUPAC.unambiguous_dna)    
    coding_rna = coding_dna.transcribe()
    protein_seq = coding_rna.translate()

    oligo = oms.NASequence.fromString(str(coding_rna))
    aaseq = oms.AASequence.fromString(str(protein_seq))

    print("The RNA sequence", str(oligo), "has mass", oligo.getMonoWeight(), "and \n"
      "translates to the protein sequence", str(aaseq), "which has mass", aaseq.getMonoWeight() )