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Sample an alignment to a fixed length
-------------------------------------
Let's load in an alignment of rodents to use in the examples.
.. jupyter-execute::
:raises:
from cogent3 import get_app
loader = get_app("load_aligned", moltype="protein", format="phylip")
aln = loader("data/abglobin_aa.phylip")
aln
How to sample the first ``n`` positions of an alignment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
We can use the ``fixed_length`` app to sample an alignment to a fixed length. By default, it will sample from the beginning of an alignment, the argument ``length=20`` specifies how many positions to sample.
.. jupyter-execute::
:raises:
from cogent3 import get_app
first_20 = get_app("fixed_length", length=20)
first_20(aln)
How to sample ``n`` positions from within an alignment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Creating the ``fixed_length`` app with the argument ``start=x`` specifies that the sampled sequence should begin ``x`` positions into the alignment.
.. jupyter-execute::
:raises:
from cogent3 import get_app
skip_10_take_20 = get_app("fixed_length", length=20, start=10)
skip_10_take_20(aln)
How to sample ``n`` positions randomly from within an alignment
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The start position can be selected at random with ``random=True``. An optional ``seed`` can be provided to ensure the same start position is used when the app is called.
.. jupyter-execute::
:raises:
from cogent3 import get_app
random_20 = get_app("fixed_length", length=20, random=True)
random_20(aln)
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