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Removing degenerate characters
------------------------------
Degenerate IUPAC base symbols represent a site position that can have multiple possible characters. For a DNA example, "Y" represents pyrimidines where the site can be either "C" or "T".
.. note:: In many molecular evolutionary and phylogenetic analyses, the gap character "-" is treated "N", meaning any base.
Let's create sample data with degenerate characters
.. jupyter-execute::
:raises:
from cogent3 import make_aligned_seqs
aln = make_aligned_seqs({"s1": "ACGA-GACG", "s2": "GATGATGYT"}, moltype="dna")
aln
Omit aligned columns containing a degenerate character
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
:raises:
from cogent3 import get_app
omit_degens = get_app("omit_degenerates", moltype="dna")
result = omit_degens(aln)
result
Omit all degenerate characters except gaps from an alignment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If we create the app with the argument ``gap_is_degen=False``, we can omit degenerate characters but retain gaps.
.. jupyter-execute::
:raises:
from cogent3 import get_app
omit_degens_keep_gaps = get_app("omit_degenerates", moltype="dna", gap_is_degen=False)
result = omit_degens_keep_gaps(aln)
result
Omit k-mers which contain degenerate characters
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
If we create ``omit_degenerates`` with the argument ``motif_length``, it will split sequences into non-overlapping tuples of the specified length and exclude any tuple that contains a degenerate character.
.. jupyter-execute::
:raises:
from cogent3 import get_app
omit_degenerates_app = get_app("omit_degenerates", moltype="dna", motif_length=2)
result = omit_degenerates_app(aln)
result
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