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bio-format-conversion

Maintainer FreedomIntelligence · Last updated April 1, 2026

Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.

OpenClawNanoClawAnalysisReproductionbio-format-conversion🧬 bioinformatics (gptomics bio-* suite)bioinformatics — sequencing & read qcconvert

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Python: SeqIO.convert() for direct conversion, or SeqIO.parse() + SeqIO.write() when modifications are needed (BioPython).
  • CLI: seqkit seq (SeqKit) for FASTA/FASTQ; samtools view for SAM/BAM/CRAM.
  • Convert this file to a different format" → Read records in one format, optionally add missing annotations, and write in the target format. Python: SeqIO.convert() for direct conversion, or SeqIO.parse() + SeqIO.write() when modifications are needed (BioPython) CLI: seqkit seq (SeqKit) for FASTA/FASTQ; samtools view for SAM/BAM/CRAM.
  • Convert sequence files between formats using Biopython's Bio.SeqIO module.

Source Doc

Excerpt From SKILL.md

SeqIO.convert() - Direct Conversion

Convert between formats in a single call. Most efficient method.

Parameters:

  • in_file - Input filename or handle
  • in_format - Input format string
  • out_file - Output filename or handle
  • out_format - Output format string

Returns: Number of records converted

Common Conversions

FromToNotes
GenBankFASTALoses annotations, keeps sequence
FASTAGenBankNeed to add molecule_type
FASTQFASTALoses quality scores
FASTAFASTQNeed to add quality scores
GenBankEMBLUsually works directly
StockholmFASTAAlignment 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+):

Use cases

  • Use when changing file formats or preparing data for different tools.

Not for

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

Upstream Related Skills

  • 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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