bio-batch-processing

npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-batch-processing --agent claude-code

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

## Version Compatibility Reference examples tested with: BioPython 1.83+ 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. # Batch Processing **"Process all my sequence files in a directory"** → Iterate, merge, split, convert, and generate summary statistics across multiple sequence files. - Python: `SeqIO.parse()`, `Path.glob()` (BioPython, pathlib) Process multiple sequence files efficiently using Biopython. ## Required Imports ```python from pathlib import Path from Bio import SeqIO ``` ## Process Multiple Files ### Iterate Over Files in Directory ```python from pathlib import Path for fasta_file in Path('data/').glob('*.fasta'): records = list(SeqIO.parse(fasta_file, 'fasta')) print(f'{fasta_file.name}: {len(records)} sequences') ``` ### Process All FASTQ Files ```python for fq_file in Path('.').glob('*.fastq'): count = sum(1 for _ in SeqIO.parse(fq_file, 'fastq')) print(f'{fq_file.name}: {count} reads') ``` ###