Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-compressed-files

Maintainer FreedomIntelligence · Last updated April 1, 2026

Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with.gz or.bz2 sequence files. Use BGZF for indexable compressed files.

OpenClawNanoClawAnalysisReproductionbio-compressed-files🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcread

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-compressed-files

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

gzip: gzip.open(path, 'rt') (Python stdlib).
bzip2: bz2.open(path, 'rt') (Python stdlib).
BGZF: bgzf.open(path, 'rt') (BioPython) or direct SeqIO.parse(path, fmt).
Handle gzip, bzip2, and BGZF compressed sequence files with Biopython.
Read a compressed sequence file" → Open a compressed file handle in text mode, then parse with the standard SeqIO interface. gzip: gzip.open(path, 'rt') (Python stdlib) bzip2: bz2.open(path, 'rt') (Python stdlib) BGZF: bgzf.open(path, 'rt') (BioPython) or direct SeqIO.parse(path, fmt).

Source Doc

Excerpt From SKILL.md

Reading Compressed Files

Goal: Parse sequence records from compressed files without decompressing to disk.

Approach: Open a decompression handle in text mode ('rt'), then pass the handle to SeqIO.parse(). The parser works identically to uncompressed input.