Filter sequence collections and alignments by length

Let’s load a collection of globin sequences. Note that we must have a the molecular type specified.

from cogent3 import get_app

loader = get_app("load_unaligned", moltype="dna", format_name="fasta")
aln = loader("data/SCA1-cds.fasta")
aln

	0
Mouse Lemur	ATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGTGAGATCCCC
Rat	ATGAAATCTAACCAAGAGCGGAGCAATGAATGCCTGCCTCCCAAGAAACGTGAGATCCCC
Mouse	ATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAACGTGAGATCCCC
Macaque	ATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGCGAGATCCCC
Chimp	ATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGCGAGATCCCC
Human	ATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGCGAGATCCCC

6 x {min=2367, median=2401.5, max=2445} dna sequence collection

Remove sequences shorter than a minimum length

Creating the min_length app and providing a positional argument specifying the minimum length allows us to filter an alignment, removing sequences which do not satisfy our threshold.

For instance, we can remove sequences from the globin alignment which are shorter than 240 amino acids long.

from cogent3 import get_app

over_240s = get_app("min_length", 240)
aln_fltrd = over_240s(aln)
aln_fltrd

	0
Mouse Lemur	ATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGTGAGATCCCC
Rat	ATGAAATCTAACCAAGAGCGGAGCAATGAATGCCTGCCTCCCAAGAAACGTGAGATCCCC
Mouse	ATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAACGTGAGATCCCC
Macaque	ATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGCGAGATCCCC
Chimp	ATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGCGAGATCCCC
Human	ATGAAATCCAACCAAGAGCGGAGCAACGAATGCCTGCCTCCCAAGAAGCGCGAGATCCCC

6 x {min=2367, median=2401.5, max=2445} dna sequence collection

Using the min_length app to filter multiple alignments

min_length is a useful app to use in data processing pipelines where downstream analysis requires sequences that exceed a given length.

In the following example, we compose a process that loads alignments and removes aligments less than 300 nucleotides in length, before writing them to a data store. We apply this process to a data store of the fasta files in the data directory. We restrict this data store to two members as a minimum example.

from cogent3 import get_app, open_data_store

dstore = open_data_store("data", suffix="fasta", limit=2)

reader = get_app("load_aligned", format_name="fasta", moltype="dna")
min_length = get_app("min_length", 300)
out_dstore = open_data_store(path_to_dir, mode="w", suffix="fasta")
writer = get_app("write_seqs", out_dstore)

process = reader + min_length + writer
result = process.apply_to(dstore)
result.describe

describe

Condition	Value
completed	1
not_completed	1
logs	1

3 rows x 2 columns