This release is a pre-release and may not be stable for production use.
tpixel
Pixel-block alignment viewer for hundreds of sequences. Renders Roark-style PIXEL plots: grey=match, red=substitution, black=gap.
Install
pip install tpixel
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.
1 maintainer
Metadata
1 maintainer
Release files for tpixel 0.1.5.dev0
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Total release size: 185.1 kB
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