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pysam
75 / 100 · Review before installing
Check before installing. Some of what it can do is expected: a data skill usually connects to databases or online services with your credentials.
By roohe/agentic-super-skills (GitHub) · data · 10 stars · scanned at commit f483e54
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
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.
Found in 1 place.
Runs commands on your computer
The author does not mention this.
Found in 1 place.
Connects to the internet
The author does not mention this. Expected for a data skill.
Found in 48 places.
Show 17 more
- skills_library/pysam/SKILL.md, line 164
**Exception:** Region strings in `fetch()` follow samtools convention (1-based): - skills_library/pysam/SKILL.md, line 166
samfile.fetch("chr1", 999, 2000) # 0-based: positions 999-1999 - skills_library/pysam/SKILL.md, line 167
samfile.fetch("chr1:1000-2000") # 1-based string: positions 1000-2000 - skills_library/pysam/SKILL.md, line 181
Without an index, use `fetch(until_eof=True)` for sequential reading. - skills_library/pysam/SKILL.md, line 207
3. **Partial overlaps:** `fetch()` returns reads overlapping region boundaries, not just those fully contained - skills_library/pysam/references/alignment_files.md, line 62
for read in samfile.fetch("chr1", 1000, 2000): - skills_library/pysam/references/alignment_files.md, line 66
for read in samfile.fetch("chr1"): - skills_library/pysam/references/alignment_files.md, line 70
for read in samfile.fetch(until_eof=True): - skills_library/pysam/references/alignment_files.md, line 79
- For unmapped reads, use `fetch("*")` or `until_eof=True` - skills_library/pysam/references/alignment_files.md, line 87
iter1 = samfile.fetch("chr1", 1000, 2000) - skills_library/pysam/references/alignment_files.md, line 88
iter2 = samfile.fetch("chr2", 5000, 6000) - skills_library/pysam/references/alignment_files.md, line 163
for read in samfile.fetch("chr1", 1000, 2000): - skills_library/pysam/references/alignment_files.md, line 247
**Exception:** Region strings in `fetch()` and `pileup()` follow samtools conventions (1-based): - skills_library/pysam/references/alignment_files.md, line 250
samfile.fetch("chr1", 999, 2000) # Python style: 0-based - skills_library/pysam/references/alignment_files.md, line 251
samfile.fetch("chr1:1000-2000") # samtools style: 1-based - skills_library/pysam/references/alignment_files.md, line 270
3. **Use `fetch(until_eof=True)` for sequential reading** of non-indexed files - skills_library/pysam/references/alignment_files.md, line 276
1. **Partial overlaps:** `fetch()` returns reads that overlap region boundaries—implement explicit filtering if exact boundaries are needed
and 28 more places
Safer alternatives
Low-risk skills in the same category (data) that look related. Check that one does what you need.
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=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/roohe/agentic-super-skills' "$d" && git -C "$d" checkout --quiet 'f483e54f3ad5f202a77d45f2e57f8d970b71195f' -- 'skills_library/pysam' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills_library/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 roohe/agentic-super-skills shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/roohe/agentic-super-skills/)
Score history
| Date | Version | Score |
|---|
| 2026-11-08 | f483e54 | 75 |
Also found in
Identical copies of this skill exist at:
- BioTender-max/awesome-bio-agent-skills/skills/kdense/pysam