bio-compressed-files

npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-compressed-files --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

## Version Compatibility Reference examples tested with: BioPython 1.83+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Compressed Files 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)` **"Make a compressed file indexable"** → Convert to BGZF format. Only BGZF supports `SeqIO.index()` on compressed data. ## Required Imports ```python import gzip import bz2 from Bio import SeqIO from Bio import bgzf ``` ## Reading Compressed Files **Goal:** Parse sequence records from compressed files without decompressing to disk. **Approach:** Open a decompression handle in text mode (`'rt'`