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pysam
79 / 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 Xircth/VibeX (GitHub) · coding · 206 stars · scanned at commit 457d352
Python/HTSlib workflows for genomic files. Use when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.
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 2 places.
Runs commands on your computer
This is disclosed by the author in the skill's SKILL.md or README. Expected for a coding skill.
Found in 2 places.
Connects to the internet
This is disclosed by the author in the skill's SKILL.md or README.
Found in 72 places.
Show 17 more
- plugins/science/contents/skills/pysam/SKILL.md, line 93
bam.fetch(region="chr1:100-199") # 1-based inclusive - plugins/science/contents/skills/pysam/SKILL.md, line 115
for read in bam.fetch("chr1", 1_000, 2_000): - plugins/science/contents/skills/pysam/SKILL.md, line 125
Use `fetch(until_eof=True)` to stream every record in file order, including - plugins/science/contents/skills/pysam/SKILL.md, line 130
for read in bam.fetch(until_eof=True): - plugins/science/contents/skills/pysam/SKILL.md, line 136
- `fetch()` returns alignment records overlapping a region. - plugins/science/contents/skills/pysam/SKILL.md, line 174
for record in variants.fetch("chr1", 999_999, 2_000_000): - plugins/science/contents/skills/pysam/SKILL.md, line 203
sequence = fasta.fetch("chr1", 999, 1_099) - plugins/science/contents/skills/pysam/SKILL.md, line 224
for interval in tbx.fetch("chr1", 1_000, 2_000): - plugins/science/contents/skills/pysam/SKILL.md, line 247
for read in cram.fetch("chr1", 1_000, 2_000): - plugins/science/contents/skills/pysam/SKILL.md, line 320
- Treating numeric `VariantFile.fetch()` coordinates as 1-based - plugins/science/contents/skills/pysam/SKILL.md, line 323
- Assuming `fetch()` includes unplaced unmapped alignments - plugins/science/contents/skills/pysam/references/alignment_files.md, line 72
for read in bam.fetch("chr1", 1_000, 2_000): - plugins/science/contents/skills/pysam/references/alignment_files.md, line 80
- `fetch()` with no region still requires an index and returns mapped records. - plugins/science/contents/skills/pysam/references/alignment_files.md, line 86
for read in bam.fetch(until_eof=True): - plugins/science/contents/skills/pysam/references/alignment_files.md, line 95
`fetch("*")` requests only unplaced unmapped records at the end of a - plugins/science/contents/skills/pysam/references/alignment_files.md, line 100
`multiple_iterators` belongs to `fetch()`, not the `AlignmentFile` - plugins/science/contents/skills/pysam/references/alignment_files.md, line 105
chr1_reads = bam.fetch("chr1", multiple_iterators=True)
and 52 more places
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=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/Xircth/VibeX' "$d" && git -C "$d" checkout --quiet '457d3525a3554fe9a867feb946c69c830c541fce' -- 'plugins/science/contents/skills/pysam' && mkdir -p ~/.agents/skills && cp -R "$d"/'plugins/science/contents/skills/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 Xircth/VibeX shows the score of its lowest-scoring skill.
[](https://zalavijaysinh.github.io/skilltrust/repos/Xircth/VibeX/)
Score history
| Date | Version | Score |
|---|
| 2026-11-13 | 457d352 | 79 |
| 2026-11-08 | eb30591 | 100 |
Also found in
Identical copies of this skill exist at:
- sharkrebel/everything-everywhere-for-antigravity/skills/pysam