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bio-genome-intervals-gtf-gff-handling

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Parse and manipulate GTF/GFF annotation files.

OpenClawNanoClaw分析处理复现实验bio-genome-intervals-gtf-gff-handling🧠 bioos extended suitebioos extended bioinformatics suiteparse

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-genome-intervals-gtf-gff-handling

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

2 min

核心说明

  • GTF 、 GFF3 are standard gene annotation formats. Both use 1-based coordinates。
  • df = gtfparse.read_gtf('annotation.gtf')。

原始文档

SKILL.md 摘录

Format Comparison

FeatureGTFGFF3
Coordinate system1-based, inclusive1-based, inclusive
HierarchyImplicit (gene_id, transcript_id)Explicit (Parent attribute)
Attribute formatkey "value";key=value;
Comments##
Fasta sequencesNot standard##FASTA directive

Filter by feature type

genes = df[df['feature'] == 'gene'] transcripts = df[df['feature'] == 'transcript'] exons = df[df['feature'] == 'exon']

Get specific gene

gene_df = df[df['gene_name'] == 'TP53']

适用场景

  • Use bio-genome-intervals-gtf-gff-handling ，用于 genomics 、 bioinformatics workflows。
  • Apply bio-genome-intervals-gtf-gff-handling to sequencing，variant，或 omics analysis tasks。

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

  • bed-file-basics - BED format and conversion
  • interval-arithmetic - Gene/exon overlap analysis
  • proximity-operations - TSS proximity analysis
  • differential-expression/de-results - Gene coordinate mapping

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