Pysam sam bam summary starter

Skill ma-compbio-lab/SkillFoundry/skills/genomics/pysam-sam-bam-summary-starter

A framework for discovering, compiling, and validating reusable skills for scientific agents.

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill pysam-sam-bam-summary-starter

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.2 KB, as published. Nobody here has run it

pysam SAM BAM Summary Starter

Use this skill to read a small SAM, BAM, or CRAM file with pysam, summarize core alignment statistics, and optionally emit an indexed BAM artifact for downstream debugging or demos.

What it does

Opens a local alignment file with pysam.AlignmentFile.
Reports header references, mapped and unmapped counts, pairing flags, and per-reference mapped counts.
Optionally writes a BAM copy and builds a .bai index.

When to use it

You need a deterministic starter for SAM/BAM/CRAM handling in Python.
You want a tiny verified example of format conversion plus indexing.
You need a compact JSON summary before building larger alignment-processing skills.

Example

slurm/envs/genomics/bin/python skills/genomics/pysam-sam-bam-summary-starter/scripts/run_pysam_sam_bam_summary.py \
  --input skills/genomics/pysam-sam-bam-summary-starter/examples/toy_reads.sam \
  --out scratch/genomics/pysam_summary.json \
  --bam-out scratch/genomics/toy_reads.bam

Verification