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SKILL verified MIT Self-run

Bio Sequence Io Manipulation

skill-onescience-ai-oneskills-sequence-io-manipulation · by onescience-ai

序列读写与操作 skill。用于 FASTA、FASTQ、GenBank、EMBL、GFF/GTF、PDB/mmCIF 中的序列解析、格式转换、反向互补、转录翻译、GC/长度统计、motif 搜索、批量序列处理和序列抽取。

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Install

$ agentstack add skill-onescience-ai-oneskills-sequence-io-manipulation

✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

View the full security report →

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Reliability & compatibility

✓ Security review passed
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Declared compatibility

Claude CodeClaude Desktop

Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.

Preview Execution monitoring

We're building live execution health for every listing: tool-call success rate, median latency, uptime, and last-checked timestamps, measured, not self-reported. It isn't live yet, so we don't show numbers we can't stand behind.

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About

序列读写与操作

使用边界

用于 sequence-level 操作。若涉及 read-level QC 进入 read-qc-trimming；若涉及比对后的 BAM/CRAM 进入 alignment-bam-processing。

推荐流程

  1. 确认输入格式、压缩方式、序列 ID 规则和文件大小。
  2. 读取方式：
  • 小文件可一次性读取。
  • 大 FASTA/FASTQ 使用索引或流式迭代。
  1. 操作类型：
  • 统计：长度、GC、N 比例、quality。
  • 转换：FASTA/FASTQ/GenBank/GFF 互转。
  • 生物学变换：reverse complement、transcribe、translate、ORF/motif。
  • feature 提取：CDS、gene、exon、protein。
  1. 输出新文件时保留 ID 映射和过滤日志。

交接物

bio_task_family: sequence-io
input_format:
output_format:
sequence_type: dna | rna | protein | mixed
operation:
id_handling:
validation_checks:
expected_outputs:
execution_entry:

禁止事项

  • 不要用临时字符串切分解析复杂 GenBank/GFF；使用结构化解析思路。
  • 不要在未确认遗传密码表时翻译非标准生物。
  • 不要丢失原始 record ID 和坐标映射。

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

Install and usage instructions live in the source repository linked above.

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Versions

  • v0.1.0 Imported from the upstream source.

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