AG
Data & Repro
agent-browser
Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test w…
FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-filter-sequences
Maintainer FreedomIntelligence · Last updated April 1, 2026
Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by specific criteria.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-filter-sequences
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Python: generator expression with SeqIO.parse() + SeqIO.write() (BioPython).
- CLI: seqkit seq -m 200 (SeqKit) or awk on FASTA.
- 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.
Source Doc
Excerpt From SKILL.md
Core Pattern
Use generator expressions for memory-efficient filtering:
Select from ID File
Goal: Extract sequences whose IDs appear in an external list file.
Approach: Load IDs into a set for O(1) lookup, then stream-filter and write matches.
Reference (BioPython 1.83+):
Combine Multiple Filters
Goal: Remove sequences that fail any of several quality/content thresholds.
Approach: Define a predicate function that checks all criteria, apply it as a generator filter, and write survivors.
Reference (BioPython 1.83+):
Use cases
- Use when subsetting sequences, removing unwanted records, or selecting by specific criteria.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- read-sequences - Parse sequences before filtering
- write-sequences - Write filtered sequences to output
- fastq-quality - Filter FASTQ by quality scores
- paired-end-fastq - Synchronized filtering of paired reads
- sequence-manipulation/motif-search - Filter by complex motif patterns
- alignment-files - Filter aligned reads with samtools view -f/-F
Related skills
Related skills
AL
Data & Repro
alpha-vantage
Access 20+ years of global financial data: equities, options, forex, crypto, commodities, economic indicators, and 50+ technical indicators.
K-Dense-AI/claude-scientific-skillsView
BI
Data & Repro
bio-alignment-filtering
Filter alignments by flag, quality, region, or paired status.
FreedomIntelligence/OpenClaw-Medical-SkillsView
BI
Data & Repro
bio-alignment-indexing
Index BAM/CRAM files with samtools index for random access.
FreedomIntelligence/OpenClaw-Medical-SkillsView