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bio-write-sequences

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

Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modified records.

OpenClawNanoClaw分析处理复现实验bio-write-sequences🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcwrite

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-write-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

2 min

核心说明

  • Python：SeqIO.write() (BioPython)。
  • R：writeXStringSet() (Biostrings)。
  • 撰写 sequences to file" → Serialize SeqRecord objects into formatted sequence file. Python：SeqIO.write() (BioPython) R：writeXStringSet() (Biostrings)。
  • 撰写 SeqRecord objects to sequence files ，使用 Biopython's Bio.SeqIO module。

原始文档

SKILL.md 摘录

SeqIO.write() - Write Records to File

Write one or more SeqRecord objects to a file.

Parameters:

  • records - Single SeqRecord, list, or iterator of SeqRecords
  • handle - Filename (string) or file handle
  • format - Output format string

Returns: Number of records written (integer)

record.format() - Get Formatted String

Get a string representation without writing to file.

Creating SeqRecord Objects

Goal: Construct in-memory sequence records suitable for writing to any format.

Approach: Create SeqRecord with at minimum a Seq and id. Add letter_annotations for FASTQ, annotations['molecule_type'] for GenBank/EMBL.

"Create a sequence record from scratch" → Wrap a Seq string in a SeqRecord with metadata fields.

  • Python: SeqRecord(Seq(...), id=...) (BioPython)

适用场景

  • 适合在saving sequences，creating new sequence files，或 outputting modified records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 - Read sequences before modifying and writing
  • format-conversion - Direct format conversion without intermediate processing
  • filter-sequences - Filter sequences before writing subset
  • sequence-manipulation/seq-objects - Create SeqRecord objects to write
  • alignment-files - For SAM/BAM output, use samtools/pysam

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