pysam

55 / 100 · Review before installing

Check before installing. Some of what it can do is expected: a coding skill usually runs build and test commands.

By anubhavg-icpl/vibe (GitHub) · coding · 13 stars · scanned at commit d51e7ac

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines. Use when you need help with pysam.

Works with any agent that supports SKILL.md skills.

What this skill can do

Downloads and installs other software

The author does not mention this. It runs automatically when the plugin is installed.

Found in 11 places.

skills/sci-pysam/SKILL.md, line 31uv pip install pysam
.claude/settings.json, line 166"Bash(npx @claude-flow*)",
.claude/settings.json, line 167"Bash(npx claude-flow*)",

Show 8 more

.mcp.json, line 4"command": "npx",
hooks/cmods/README.md, line 96npx eslint --fix "$FILE" 2>/dev/null
hooks/cmods/post-edit-format.sh, line 29npx prettier --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/post-edit-format.sh, line 32npx biome format --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/post-edit-format.sh, line 80npx prettier --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/post-edit-format.sh, line 86npx prettier --write "$FILE" 2>/dev/null && FORMATTED=true
hooks/cmods/pre-commit-lint.sh, line 38echo "$files" | xargs npx eslint --max-warnings 0 2>/dev/null
hooks/hooks.json, line 106"command": "#!/bin/bash\n# Run TypeScript check after editing TS files\ninput=$(cat)\nfile_path=$(echo \"$input\" | jq -r '.tool_input.file_path // \"\"')\n\nif

Runs commands on your computer

The author does not mention this. It runs automatically when the plugin is installed. Expected for a coding skill.

Found in 63 places.

skills/sci-pysam/SKILL.md, line 31uv pip install pysam
.claude/settings.json, line 9"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" pre-bash'",
.claude/settings.json, line 19"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" pre-edit'",

Show 17 more

.claude/settings.json, line 31"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" post-edit'",
.claude/settings.json, line 41"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" post-bash'",
.claude/settings.json, line 52"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" route'",
.claude/settings.json, line 63"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" session-restore'",
.claude/settings.json, line 68"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/auto-memory-hook.mjs\" import'",
.claude/settings.json, line 79"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" session-end'",
.claude/settings.json, line 90"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/auto-memory-hook.mjs\" sync'",
.claude/settings.json, line 102"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" compact-manual'"
.claude/settings.json, line 106"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" session-end'",
.claude/settings.json, line 116"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" compact-auto'"
.claude/settings.json, line 120"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" session-end'",
.claude/settings.json, line 131"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" status'",
.claude/settings.json, line 142"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" post-task'",
.claude/settings.json, line 153"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/hook-handler.cjs\" notify'",
.claude/settings.json, line 162"command": "sh -c 'exec node \"${CLAUDE_PROJECT_DIR:-.}/.claude/helpers/statusline.cjs\"'"
.mcp.json, line 4"command": "npx",
hooks/cmods/README.md, line 64"os.system("

and 43 more places

Connects to the internet

The author does not mention this.

Found in 48 places.

skills/sci-pysam/SKILL.md, line 42for read in samfile.fetch("chr1", 1000, 2000):
skills/sci-pysam/SKILL.md, line 60sequence = fasta.fetch("chr1", 1000, 2000)
skills/sci-pysam/SKILL.md, line 83- Region-based fetching with `fetch()`

Show 17 more

skills/sci-pysam/SKILL.md, line 164**Exception:** Region strings in `fetch()` follow samtools convention (1-based):
skills/sci-pysam/SKILL.md, line 166samfile.fetch("chr1", 999, 2000) # 0-based: positions 999-1999
skills/sci-pysam/SKILL.md, line 167samfile.fetch("chr1:1000-2000") # 1-based string: positions 1000-2000
skills/sci-pysam/SKILL.md, line 181Without an index, use `fetch(until_eof=True)` for sequential reading.
skills/sci-pysam/SKILL.md, line 2073. **Partial overlaps:** `fetch()` returns reads overlapping region boundaries, not just those fully contained
skills/sci-pysam/references/alignment_files.md, line 62for read in samfile.fetch("chr1", 1000, 2000):
skills/sci-pysam/references/alignment_files.md, line 66for read in samfile.fetch("chr1"):
skills/sci-pysam/references/alignment_files.md, line 70for read in samfile.fetch(until_eof=True):
skills/sci-pysam/references/alignment_files.md, line 79- For unmapped reads, use `fetch("*")` or `until_eof=True`
skills/sci-pysam/references/alignment_files.md, line 87iter1 = samfile.fetch("chr1", 1000, 2000)
skills/sci-pysam/references/alignment_files.md, line 88iter2 = samfile.fetch("chr2", 5000, 6000)
skills/sci-pysam/references/alignment_files.md, line 163for read in samfile.fetch("chr1", 1000, 2000):
skills/sci-pysam/references/alignment_files.md, line 247**Exception:** Region strings in `fetch()` and `pileup()` follow samtools conventions (1-based):
skills/sci-pysam/references/alignment_files.md, line 250samfile.fetch("chr1", 999, 2000) # Python style: 0-based
skills/sci-pysam/references/alignment_files.md, line 251samfile.fetch("chr1:1000-2000") # samtools style: 1-based
skills/sci-pysam/references/alignment_files.md, line 2703. **Use `fetch(until_eof=True)` for sequential reading** of non-indexed files
skills/sci-pysam/references/alignment_files.md, line 2761. **Partial overlaps:** `fetch()` returns reads that overlap region boundaries—implement explicit filtering if exact boundaries are needed

and 28 more places

Reads your saved credentials, such as SSH keys or .env files

The author does not mention this. It runs automatically when the plugin is installed.

Found in 1 place.

hooks/cmods/dangerous-cmd-warn.sh, line 79PATTERNS["cat\s+.*\\.env"]="Displaying .env file may expose secrets"

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'pysam' ] || [ -L ~/.agents/skills/'pysam' ]; then echo 'A skill folder named pysam already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/anubhavg-icpl/vibe' "$d" && git -C "$d" checkout --quiet 'd51e7ac9a34111cd2e63daed83c2198f91570050' -- 'skills/sci-pysam' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/sci-pysam' ~/.agents/skills/'pysam' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'pysam' ~/.claude/skills/'pysam' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

Badge for your README

The badge for anubhavg-icpl/vibe shows the score of its lowest-scoring skill.

SkillTrust badge for anubhavg-icpl/vibe

[![SkillTrust](https://zalavijaysinh.github.io/skilltrust/badges/anubhavg-icpl/vibe.svg)](https://zalavijaysinh.github.io/skilltrust/repos/anubhavg-icpl/vibe/)

Score history

Date	Version	Score
2026-11-08	`d51e7ac`	55