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bio-write-sequences

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionbio-write-sequences🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcwrite

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

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

Source Doc

Excerpt From SKILL.md

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)

Use cases

  • Use when saving sequences, creating new sequence files, or outputting modified records.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • 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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