bio-format-conversion
Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-format-conversion --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Format Conversion **"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. ## Required Import ```python from Bio import SeqIO ``` ## Core Function ### SeqIO.convert() - Direct Conversion Convert between formats in a single call. Most efficient method. ```python count = SeqIO.convert('input.gb', 'genbank', 'output.fasta', 'fasta') print(f'Converted {count} records') ``` **Parameters:** - `in_file` - Input filename o
- Version Compatibility
- Required Import
- Core Function
- SeqIO.convert() - Direct Conversion
- Common Conversions
- Code Patterns
- Simple Conversion
- GenBank to FASTA
- FASTQ to FASTA (drop quality)
- FASTA to GenBank (requires moleculetype)
- FASTA to FASTQ (add dummy quality)
- Batch Convert Multiple Files
- Convert with Modifications
- Alignment Format Conversion
What does the bio-format-conversion skill do?
Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-format-conversion --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.