react-msaview-cli 5.10.0 → 6.1.0
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- package/README.md +26 -5
- package/package.json +3 -3
package/README.md
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@@ -94,16 +94,33 @@ is byte-for-byte compatible with the `interproscan` command.
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#### Options
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| Option | Description
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| --------------------- |
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| `-o, --output <file>` | Output GFF file path
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| `--database <name>` | InterPro member db to read
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| Option | Description | Default |
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| --------------------- | --------------------------------- | ------------- |
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| `-o, --output <file>` | Output GFF file path | `domains.gff` |
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| `--database <name>` | InterPro member db to read | `pfam` |
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| `--no-cache` | Re-fetch, ignoring the disk cache | off |
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```bash
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react-msaview-cli interpro accessions.tsv -o domains.gff
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react-msaview-cli interpro accessions.tsv -o domains.gff --database cdd
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```
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#### Caching
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The InterPro API serves one protein per request — there is no batch endpoint —
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so the request count is fixed at one per distinct accession. To keep that from
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being paid twice, every response is cached on disk under
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`$XDG_CACHE_HOME/react-msaview-cli/interpro` (override with
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`REACT_MSAVIEW_CACHE`), keyed by InterPro release so a new release misses
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cleanly rather than serving coordinates computed against the old one. Proteins
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with no matches are cached too, so they are not re-fetched every run.
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A re-run of the same dataset therefore makes one request — the release lookup —
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and answers the rest from disk. That also makes a failed run resumable: retries
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are automatic with backoff, and if the API is still unreachable the accessions
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already fetched stay cached, so re-running picks up where it stopped instead of
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asking EBI for all of them again.
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### genestructure
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Build a **gene-structure GFF** for a coding-sequence alignment from a RefSeq
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@@ -276,9 +293,13 @@ seq2 InterProScan protein_match 5 120 . . . Name=PF00001;signature_desc=7tm_1;de
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After generating the GFF file, you can load it in react-msaview:
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- Open your MSA file in react-msaview
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-
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- Select the generated GFF file in the import form's **Annotation GFF file or
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URL** field
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- Domains appear as colored boxes on the alignment
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The **Annotations > Open InterProScan results...** menu item takes InterProScan
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JSON rather than GFF, so use the import form for the file generated above.
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In the React component, pass it inline as the `gff` prop (see the "Protein
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domains" example in `packages/examples`):
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package/package.json
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@@ -1,6 +1,6 @@
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{
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"name": "react-msaview-cli",
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"version": "
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"version": "6.1.0",
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"license": "MIT",
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"type": "module",
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"repository": {
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@@ -28,8 +28,8 @@
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"mobx-react": "^10.0.0",
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"react": "^19.2.8",
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"react-dom": "^19.2.8",
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"msa-parsers": "
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"react-msaview": "
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"msa-parsers": "6.1.0",
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"react-msaview": "6.1.0"
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},
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"scripts": {
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"clean": "node --eval \"fs.rmSync('dist',{recursive:true,force:true})\" --input-type=module",
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