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bio-format-conversion
维护者 FreedomIntelligence · 最近更新 2026年4月1日
Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-format-conversion
- 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：SeqIO.convert() ，用于 direct conversion，或 SeqIO.parse() + SeqIO.write() when modifications are needed (BioPython)。
- CLI：seqkit seq (SeqKit) ，用于 FASTA/FASTQ；samtools view ，用于 SAM/BAM/CRAM。
- Convert this file to different format" → Read records in one format，optionally add missing annotations，、 write in target format. Python：SeqIO.convert() ，用于 direct conversion，或 SeqIO.parse() + SeqIO.write() when modifications are needed (BioPython) CLI：seqkit seq (SeqKit) ，用于 FASTA/FASTQ；samtools view ，用于 SAM/BAM/CRAM。
- Convert sequence files between formats ，使用 Biopython's Bio.SeqIO module。
原始文档
SKILL.md 摘录
SeqIO.convert() - Direct Conversion
Convert between formats in a single call. Most efficient method.
Parameters:
in_file- Input filename or handlein_format- Input format stringout_file- Output filename or handleout_format- Output format string
Returns: Number of records converted
Common Conversions
| From | To | Notes |
|---|---|---|
| GenBank | FASTA | Loses annotations, keeps sequence |
| FASTA | GenBank | Need to add molecule_type |
| FASTQ | FASTA | Loses quality scores |
| FASTA | FASTQ | Need to add quality scores |
| GenBank | EMBL | Usually works directly |
| Stockholm | FASTA | Alignment to sequences |
FASTA to GenBank (requires molecule_type)
Goal: Convert FASTA to GenBank format, which requires molecule_type annotation.
Approach: Stream records through a generator that injects the missing annotation, then write.
Reference (BioPython 1.83+):
适用场景
- 适合在changing file formats 或 preparing data ，用于 different tools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 for custom conversion logic
- write-sequences - Write converted sequences with modifications
- batch-processing - Convert multiple files at once
- compressed-files - Handle compressed input/output during conversion
- alignment-files - For SAM/BAM/CRAM conversion, use samtools view
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