tpixel 0.1.1.dev0

Pixel-block alignment viewer for hundreds of sequences (Roark-style PIXEL plots)

tpixel

Pixel-block alignment viewer for hundreds of sequences. Renders Roark-style PIXEL plots: grey=match, red=substitution, black=gap.

Install

pip install -e .

Usage

# Protein alignment (AA mode)
tpixel --fasta examples/env_protein_aligned.fasta -o examples/test_hiv_pixel.png

# Nucleotide alignment (NT mode — auto-detected)
tpixel --fasta examples/env_codon_aligned.fasta -o examples/test_hiv_nt_pixel.png

HIV mode is auto-detected when the alignment contains HxB2 and a *_ref sequence. Force with --hiv or --no-hiv. Nucleotide vs amino-acid mode is auto-detected from sequence content. Force with --nt or --aa.

Examples

Both alignments contain the same 33 sequences (HxB2, animal1_ref, and 31 sample sequences from 7 animals):

Sequence	Type
HxB2	Coordinate reference
animal1_ref	Parental lineage reference
animal1_s1 .. s7	animal1 samples (7)
animal2_s1 .. s5	animal2 samples (5)
animal3_s1 .. s8	animal3 samples (8)
animal4_s1	animal4 sample (1)
animal5_s1 .. s5	animal5 samples (5)
animal6_s1 .. s2	animal6 samples (2)
animal7_s1 .. s3	animal7 samples (3)

Protein alignment (AA)

env_protein_aligned.fasta — 887 columns of HIV-1 Env protein. Each AA = 1 pixel.

Nucleotide alignment (NT)

env_codon_aligned.fasta — 2661 columns of codon-aligned HIV-1 Env DNA. Each NT = 1 pixel. PNGS markers are detected by translating internally and mapped back to NT columns.