from cogent3 import make_aligned_seqs
aln = make_aligned_seqs({"s1": "ACGACGACG", "s2": "GATGATGAT"}, moltype="dna")
aln| 0 | |
| s1 | ACGACGACG |
| s2 | GATGATGAT |
2 x 9 dna alignment
Sample nucleotides from a given codon position
The take_codon_positions app allows you to extract all nucleotides at a given codon position from an alignment.
Let’s create a sample alignment for our example.
Extract the third codon position from an alignment
We can achieve this by creating the take_codon_positions app with 3 as a positional argument.
from cogent3 import get_app
take_pos3 = get_app("take_codon_positions", 3, moltype="dna")
result = take_pos3(aln)
result| 0 | |
| s1 | GGG |
| s2 | TTT |
2 x 3 dna alignment
Extract the first and second codon positions from an alignment
We can achieve this by creating the take_codon_positions app with 1 and 2 as a positional argument.
from cogent3 import get_app
take_pos12 = get_app("take_codon_positions", 1, 2, moltype="dna")
result = take_pos12(aln)
result| 0 | |
| s1 | ACACAC |
| s2 | GAGAGA |
2 x 6 dna alignment
Extract only the third codon positions from four-fold degenerate codons
We can achieve this by creating the take_codon_positions app with the argument fourfold_degenerate=True.
from cogent3 import get_app, make_aligned_seqs
aln_ff = make_aligned_seqs({"s1": "GCAAGCGTTTAT", "s2": "GCTTTTGTCAAT"}, moltype="dna")
take_fourfold = get_app("take_codon_positions", fourfold_degenerate=True, moltype="dna")
result = take_fourfold(aln_ff)
result| 0 | |
| s1 | AT |
| s2 | TC |
2 x 2 dna alignment
Create a composed process which samples only the third codon position
Let’s set up a data store containing all the files with the “.fasta” suffix in the data directory, limiting the data store to two members as a minimum example.
from cogent3 import open_data_store
fasta_seq_dstore = open_data_store("data", suffix="fasta", mode="r", limit=2)Now let’s set up a process composing the following apps: load_aligned (loads the sequences ), take_codon_positions (extracts the third codon position), and write_seqs (writes the filtered sequences to a data store).
Note
Learn the basics of turning apps into composed processes here!
from cogent3 import get_app, open_data_store
out_dstore = open_data_store(path_to_dir, suffix="fa", mode="w")
loader = get_app("load_aligned", format_name="fasta", moltype="dna")
cpos3 = get_app("take_codon_positions", 3)
writer = get_app("write_seqs", out_dstore, format_name="fasta")
process = loader + cpos3 + writer
Tip
When running this code on your machine, remember to replace path_to_dir with an actual directory path.
Now let’s apply process to our data store! This populates out_dstore (which is returned by the .apply_to() call) with the filtered alignments. We can index out_dstore to see individual data members. We could take a closer look using the .read() method on data members.
out_dstore = process.apply_to(fasta_seq_dstore)
out_dstore.describe| Condition | Value |
|---|---|
| completed | 1 |
| not_completed | 1 |
| logs | 1 |
3 rows x 2 columns