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BI
bio-filter-sequences
维护者 FreedomIntelligence · 最近更新 2026年4月1日
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.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-filter-sequences
- 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
核心说明
- Python：generator expression ，支持 SeqIO.parse() + SeqIO.write() (BioPython)。
- CLI：seqkit seq -m 200 (SeqKit) 或 awk on FASTA。
- Filter sequences by length，quality，或 content" → Apply boolean criteria to stream of sequence records 、 write survivors to output. Python：generator expression ，支持 SeqIO.parse() + SeqIO.write() (BioPython) CLI：seqkit seq -m 200 (SeqKit) 或 awk on FASTA。
- Filter 、 select sequences based on various criteria ，使用 Biopython。
原始文档
SKILL.md 摘录
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+):
适用场景
- 适合在subsetting sequences，removing unwanted records，或 selecting by specific criteria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 - 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
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