bio-filter-sequences

npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-filter-sequences --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. # Filter Sequences **"Filter sequences by length, quality, or content"** → Apply boolean criteria to a stream of sequence records and write survivors to output. - Python: generator expression with `SeqIO.parse()` + `SeqIO.write()` (BioPython) - CLI: `seqkit seq -m 200` (SeqKit) or `awk` on FASTA Filter and select sequences based on various criteria using Biopython. ## Required Imports ```python from Bio import SeqIO from Bio.SeqUtils import gc_fraction ``` ## Core Pattern Use generator expressions for memory-efficient filtering: ```python records = SeqIO.parse('input.fasta', 'fasta') filtered = (rec for rec in records if len(rec.seq) >= 100) SeqIO.write(filtered, 'output.fasta', 'fasta') ``` ## Filter by Length ### Minimum Length ```python records = SeqIO.parse('input.fasta', 'fas