guess-ploidy-py

name	guess-ploidy-py
description	Use when plotting `bcftools +guess-ploidy -v` output into a PNG summary of haploid, diploid, score, and site-count signals across samples.
disable-model-invocation	true
user-invocable	true

guess-ploidy-py

Quick Start

• Command: guess-ploidy.py guess-ploidy.out image-prefix
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/guess-ploidy.py
• Output: writes image-prefix.png

When To Use This Tool

• Visualize the verbose output of bcftools +guess-ploidy -v.
• Compare haploid vs diploid likelihood signals across samples.
• Inspect the total score and number-of-sites track before deciding whether ploidy calls look plausible.
• Produce a static PNG summary without opening an interactive plotting session.

Common Patterns

# 1) Plot the verbose plugin output
guess-ploidy.py guess-ploidy.out ploidy_summary

# 2) End-to-end from bcftools output to PNG
bcftools +guess-ploidy -v input.vcf.gz > guess-ploidy.out
guess-ploidy.py guess-ploidy.out cohort_x_ploidy

# 3) Inspect the generated artifact
file cohort_x_ploidy.png

Recommended Workflow

1. Run bcftools +guess-ploidy -v and keep the verbose text output file.
2. Pass that file plus an output prefix to guess-ploidy.py.
3. Open the generated PNG and inspect the male/female score separation together with the log-scaled site-count axis.
4. Re-run the upstream ploidy call if the plotted sample ordering or score separation looks suspicious.

Guardrails

• The script requires exactly two positional arguments; even --help just falls through to the generic usage message.
• It expects the verbose guess-ploidy text format and only uses rows beginning with SEX.
• Output is a static PNG only; there is no PDF / SVG option in this wrapper.
• The plot logic explicitly splits samples by sex labels M and F, so unusual or missing labels will not be grouped as intended.
• The script uses the non-interactive Matplotlib Agg backend and does not display a GUI window.