Guess Ploidy Py

# 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.