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.. jupyter-execute::
:hide-code:
import set_working_directory
Select named sequences from a collection
----------------------------------------
Let's load alignment of primates to use in examples.
.. jupyter-execute::
:raises:
from cogent3 import get_app
loader = get_app("load_aligned", moltype="dna")
aln = loader("data/primate_brca1.fasta")
aln
Selecting sequences from a collection
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Using the ``take_named_seqs`` app we can select sequences from a collection that match provided names. For instance, we could be interested in an alignment of sequences from Humans with those from our two closest relatives.
.. jupyter-execute::
:raises:
from cogent3 import get_app
greater_ape_selector = get_app("take_named_seqs", "Human", "Chimpanzee", "Gorilla")
ape_aln = greater_ape_selector(aln)
ape_aln
Using ``take_named_seqs`` in a composed app process
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. jupyter-execute::
from cogent3 import get_app
loader = get_app("load_aligned", format="fasta", moltype="dna")
select_seqs = get_app("take_named_seqs", "Human", "Rhesus", "Galago")
process = loader + select_seqs
hrg_aln = process("data/primate_brca1.fasta")
hrg_aln.names
Removing sequences from a collection
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Creating the ``take_named_seqs`` app with the argument ``negate=True`` will exclude sequences that match the provided names. For instance, perhaps the Galago has got to go.
.. jupyter-execute::
:raises:
from cogent3 import get_app
no_galagos = get_app("take_named_seqs", "Galago", negate=True)
no_galago_aln = no_galagos(hrg_aln)
no_galago_aln.names
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