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Concatenating alignments
------------------------
The ``concat`` app provides a mechanism to concatenate alignments.
.. jupyter-execute::
:raises:
from cogent3 import get_app
concat_alns_app = get_app("concat", moltype="dna")
Let's create sample alignments with matching sequence names to use in the below examples.
.. jupyter-execute::
:raises:
from cogent3 import make_aligned_seqs
aln1 = make_aligned_seqs({"s1": "AAA", "s2": "CAA", "s3": "AAA"}, moltype="dna")
aln2 = make_aligned_seqs({"s1": "GCG", "s2": "GGG", "s3": "GGT"}, moltype="dna")
aln1
.. jupyter-execute::
:raises:
aln2
How to concatenate alignments
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
By default, sequences without matching names in the corresponding alignment are omitted (``intersect=True``).
.. jupyter-execute::
:raises:
result = concat_alns_app([aln1, aln2])
result
How to concatenate alignments with missing sequences
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
By providing the argument ``intersect=False``, the ``concat`` app will include missing sequences across alignments. Missing sequences are replaced by a sequence of ``"?"``.
.. jupyter-execute::
:raises:
from cogent3 import make_aligned_seqs, get_app
concat_missing = get_app("concat", moltype="dna", intersect=False)
aln3 = make_aligned_seqs({"s4": "GCG", "s5": "GGG"}, moltype="dna")
result = concat_missing([aln1, aln3])
result
How to concatenated alignments with a delimiter ``"N"``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
You can insert an ``"N"`` character in between the concatenated sequences.
.. jupyter-execute::
:raises:
from cogent3 import get_app
concat_delim = get_app("concat", join_seq="N", moltype="dna")
result = concat_delim([aln1, aln2])
result
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