gwaspeek 0.4.0

gwaspeek: interactive terminal viewer for GWAS summary statistics

gwaspeek

• Interactive terminal Manhattan plots for GWAS summary statistics: move the view along the genome and zoom in a real TTY, inspect regions, and optionally show a protein-coding gene track when the view is a single chromosome and spans ≤ 1 Mb.
• Static one-shot renders (-s) for logs or CI.
• Column names are auto-detected from bundled formatbook-style aliases.
• Chromosome layout uses full canonical human chromosome lengths for GRCh37 or GRCh38.
• Drawing uses Unicode or --ascii.

Note: Intended for quick checks of summary statistics. Plotted positions are not exact on screen because the terminal has limited pixels (resolution).

Interactive mode (default)

Interactive mode (default) opens the live TTY viewer when you pass one input path—gwaspeek FILE or gwaspeek -i FILE. In the viewer, a / d pan the plot in smaller steps (and A / D pan in larger steps). w / s zoom out and in gently; W / S use the original coarser zoom. Arrow keys and + / - mirror the fine controls, the mouse wheel zooms at the hovered cursor position, and g jumps directly to a typed region such as chr3:45000000-46000000. Use --skip (default 3.0) to omit variants whose -log10(P) is below that value before plotting; the same threshold is the y-axis floor in the plot.

Try it

After installation, from a directory that contains the file:

gwaspeek t2d_bbj_p1e-5.txt.gz

Keys

Key	Action
a / d	Pan view left/right (fine)
A / D	Pan view left/right (coarse)
w / s	Zoom out / in (fine)
W / S	Zoom out / in (coarse)
Arrow keys	Fine pan / zoom
+ / -	Zoom in / out (fine)
Mouse wheel	Zoom at cursor position
g	Jump to region (chr:start-end)
l	Toggle lead-variant labels
t	Cycle gene track: 37 → 38 → off
v	Toggle variants-in-view list
h	Toggle help
r	Reset to full genome
q	Quit

The gene track appears only on a single-chromosome view with span ≤ 1 Mb. --gtf and --gtf38 (see CLI reference) apply only in interactive mode; static -s output ignores them. --build sets the canonical chromosome-length layout, and interactive t build switching keeps the layout aligned with the active gene-track build. The interactive viewer uses an alternate terminal screen, lazy-loads gene annotations by genome build, and renders dense cells with heavier glyphs instead of simply dropping overlapping points.

Common sizing and column flags work in interactive mode too (for example --width, --height, --skip, --sig-level):

gwaspeek sumstats.tsv \
  --sep "\t" \
  --width 120 \
  --height 32 \
  --skip 2 \
  --sig-level 5e-8

Installation

pip install gwaspeek
gwaspeek --help

Static mode (-s)

For a one-shot text snapshot (non-interactive), add -s before the path:

gwaspeek -s t2d_bbj_p1e-5.txt.gz --width 120 --ascii

Invocation at a glance

Form	Mode
gwaspeek FILE	Interactive (same as -i)
gwaspeek -i FILE	Interactive
gwaspeek -s FILE	Static

Input files

Tabular GWAS summary stats (TSV/CSV or other delimiter via --sep).

Per row you need: chromosome, base-pair position, and either P or -log10(P) (names are auto-detected; override with --chr, --pos, --p, --mlog10p). Do not pass both --p and --mlog10p. Internally rows are normalized to CHR, POS, P, and derived mlog10p.

Chromosome tokens understood by the parser include numeric 1–22, X, Y, MT, and chr-prefixed forms (e.g. chr1, chrX, chrM).

CLI reference

Option	Type	Default	Description
FILE (positional)	path	—	Same as -i FILE (interactive).
-i, --interactive FILE	path	—	Interactive viewer.
-s, --static FILE	path	—	One-shot static plot.
--sep STR	string	tab (\t)	Delimiter.
--chr NAME	string	auto	Chromosome column.
--pos NAME	string	auto	Position column.
--p NAME	string	auto	P-value column (not with --mlog10p).
--mlog10p NAME	string	auto	-log10(P) column (not with --p).
--skip FLOAT	float	3.0	Drop variants below this -log10(P); also y-axis floor.
--width INT	int	100	Width (chars): static size; interactive initial/fallback.
--height INT	int	28	Height (lines): static size; interactive initial/fallback.
--ascii	flag	off	ASCII drawing instead of Unicode.
--build {37,38}	choice	37	Canonical chromosome-length layout / default genome build.
--no-color	flag	off	Disable ANSI color in interactive status/footer lines.
--sig-level FLOAT	float	5e-8	Genome-wide line in P space.
--ymax FLOAT	float	auto	Y-axis max in -log10(P).
--gtf PATH	path	bundled GRCh37	GTF (.gz ok); interactive gene track.
--gtf38 PATH	path	—	GRCh38 GTF (.gz ok); interactive mode uses bundled gene-only GTF when omitted.
-h, --help	flag	off	Help.

Examples

# Interactive (default): positional or -i
gwaspeek tests/fixtures/sumstats_small.tsv
gwaspeek -i tests/fixtures/sumstats_small.tsv

# Static
gwaspeek -s tests/fixtures/sumstats_small.tsv
gwaspeek -s tests/fixtures/sumstats_small.tsv --build 38

# Explicit columns (flags are the same in interactive mode)
gwaspeek -s sumstats.tsv --chr CHROM --pos BP --p PVAL

# Precomputed -log10(P)
gwaspeek -s sumstats_mlog10p.tsv --chr CHR --pos POS --mlog10p LOG10P

# Narrow terminals
gwaspeek -s sumstats.tsv --ascii

Tips

• Dense sumstats: raise --skip to thin points and reduce clutter.
• Unicode is usually clearer; --ascii when the terminal cannot draw box drawing / braille well.

License

MIT.

Repository

https://github.com/Cloufield/gwaspeek