数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-compressed-files

维护者 FreedomIntelligence · 最近更新 2026年4月1日

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.

OpenClawNanoClaw分析处理复现实验bio-compressed-files🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcread

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

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

原始文档

SKILL.md 摘录

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.

Gzip (.gz) (BioPython 1.83+)

Important: Use 'rt' (read text) mode, not 'rb' (read binary).

BGZF (Block Gzip) (BioPython 1.83+)

BGZF files can be read like regular gzip, but also support indexing:

适用场景

适合在working ，支持时使用。

不适用场景

Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

上游相关技能

read-sequences - Core parsing functions used with compressed handles
write-sequences - Write to compressed output files
batch-processing - Process multiple compressed files
alignment-files - BAM files use BGZF natively; samtools handles compression

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