Select named sequences from a collection

Let’s load alignment of primates to use in examples.

from cogent3 import get_app

loader = get_app("load_aligned", moltype="dna")
aln = loader("data/primate_brca1.fasta")
aln

	0
Chimpanzee	TGTGGCACAAATACTCATGCCAGCTCATTACAGCATGAGAACAGTTTATTACTCACTAAA
Galago	.......A................................G...................
HowlerMon	...............................................G............
Rhesus	...............................................G............
Orangutan	............................................................
Gorilla	............................................................
Human	............................................................

7 x 2814 (truncated to 7 x 60) dna alignment

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.

from cogent3 import get_app

greater_ape_selector = get_app("take_named_seqs", "Human", "Chimpanzee", "Gorilla")
ape_aln = greater_ape_selector(aln)
ape_aln

	0
Chimpanzee	TGTGGCACAAATACTCATGCCAGCTCATTACAGCATGAGAACAGTTTATTACTCACTAAA
Gorilla	............................................................
Human	............................................................

3 x 2814 (truncated to 3 x 60) dna alignment

Using take_named_seqs in a composed app process

from cogent3 import get_app

loader = get_app("load_aligned", format_name="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

('Galago', 'Rhesus', 'Human')

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.

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

('Rhesus', 'Human')