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Remove problem sequences from an alignment
------------------------------------------
Using ``omit_bad_seqs`` we can eliminate sequences from an ``Alignment`` based on their gap fraction and/or the number of gaps they uniquely introduce.
Let's create a sample alignment with some gaps.
.. jupyter-execute::
:raises:
from cogent3 import make_aligned_seqs
aln = make_aligned_seqs(
{
"s1": "---ACC---TT-",
"s2": "---ACC---TT-",
"s3": "---ACC---TT-",
"s4": "--AACCG-GTT-",
"s5": "--AACCGGGTTT",
"s6": "AGAACCGGGTT-",
"s7": "------------",
},
moltype="dna",
)
Removing sequences with more than X% gaps
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Creating the ``omit_bad_seqs`` app with the argument ``gap_fraction=0.5`` will omit sequences that contain 50% or more gaps.
.. jupyter-execute::
:raises:
from cogent3 import get_app
omit_frac_05 = get_app("omit_bad_seqs", gap_fraction=0.5)
omit_frac_05(aln)
Removing sequences that contribute many gaps
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The ``quantile=0.8`` argument omits sequences that are ranked above the specified quantile with respect to the number of gaps uniquely introduced into the alignment. In the following example, sequence ``s6`` is omitted, as it uniquely introduces gaps in the first two positions of the alignment.
.. jupyter-execute::
:raises:
from cogent3 import get_app
omit_quant_08 = get_app("omit_bad_seqs", quantile=0.8)
omit_quant_08(aln)
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