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Removing highly gapped positions
--------------------------------
Using the ``omit_gap_pos`` app, we can remove position from an alignment which exceed a specified proportions of gaps.
Let's create a sample alignment with gaps.
.. jupyter-execute::
:raises:
from cogent3 import make_aligned_seqs
aln = make_aligned_seqs({"s1": "ACGA-GA-CG", "s2": "GATGATG-AT"}, moltype="dna")
aln
Removing highly gapped nucleotide positions
"""""""""""""""""""""""""""""""""""""""""""
Sites with over 99% gaps are excluded by default.
.. jupyter-execute::
:raises:
from cogent3 import get_app
omit_gap_pos_app = get_app("omit_gap_pos", moltype="dna")
result = omit_gap_pos_app(aln)
result
We can alter the threshold for the allowed fraction of gaps with the ``allowed_frac`` argument. Let's create an app that excludes all aligned sites with over 49% gaps.
.. jupyter-execute::
:raises:
omit_gap_pos_app = get_app("omit_gap_pos", allowed_frac=0.49, moltype="dna")
result = omit_gap_pos_app(aln)
result
Removing highly gapped codon positions
""""""""""""""""""""""""""""""""""""""
To eliminate any codon columns (where a column is a triple of nucleotides) that contain a gap character, we use the ``motif_length`` argument.
.. jupyter-execute::
:raises:
omit_gap_pos_app = get_app(
"omit_gap_pos", allowed_frac=0, motif_length=3, moltype="dna"
)
result = omit_gap_pos_app(aln)
result
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