Removing highly gapped positions

Using the omit_gap_pos app, we can remove position from an alignment which exceed a specified proportions of gaps.

Let’s create a sample alignment with gaps.

from cogent3 import make_aligned_seqs

aln = make_aligned_seqs({"s1": "ACGA-GA-CG", "s2": "GATGATG-AT"}, moltype="dna")
aln

	0
s2	GATGATG-AT
s1	ACGA-GA.CG

2 x 10 dna alignment

Removing highly gapped nucleotide positions

Sites with over 99% gaps are excluded by default.

from cogent3 import get_app

omit_gap_pos_app = get_app("omit_gap_pos", moltype="dna")
result = omit_gap_pos_app(aln)
result

	0
s2	GATGATGAT
s1	ACGA-GACG

2 x 9 dna alignment

We can alter the threshold for the allowed fraction of gaps with the allowed_frac argument. Let’s create an app that excludes all aligned sites with over 49% gaps.

omit_gap_pos_app = get_app("omit_gap_pos", allowed_frac=0.49, moltype="dna")
result = omit_gap_pos_app(aln)
result

	0
s1	ACGAGACG
s2	GATGTGAT

2 x 8 dna alignment

Removing highly gapped codon positions

To eliminate any codon columns (where a column is a triple of nucleotides) that contain a gap character, we use the motif_length argument.

omit_gap_pos_app = get_app(
    "omit_gap_pos", allowed_frac=0, motif_length=3, moltype="dna"
)
result = omit_gap_pos_app(aln)
result

	0
s1	ACG
s2	GAT

2 x 3 dna alignment