react-msaview-cli 5.4.1 → 5.5.0
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- package/README.md +37 -0
- package/package.json +6 -6
package/README.md
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@@ -73,6 +73,43 @@ When using `--programs`, you can specify any combination of:
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- `PIRSF` - PIR SuperFamily
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- `MobiDBLite` - Disorder prediction
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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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transcript, overlaid in react-msaview the same way InterProScan domains are. The
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exon model is fetched from the NCBI Datasets v2 API; each species' Nth exon is
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named `exon-N`, so a given exon is the same color in every row and the exon
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architecture reads straight down the alignment.
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```bash
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react-msaview-cli genestructure <input-msa> --gene <symbol> --ref <rowname> [options]
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```
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The exon boundaries of the chosen transcript are mapped onto the reference row's
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columns, then projected into every other row's own ungapped coordinates — so an
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exon that picks up a frameshifting indel in one lineage gets shorter on exactly
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that row while staying column-aligned with the rest. The reference row must be
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the transcript's coding sequence (the CLI warns if its length doesn't match).
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#### Options
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| Option | Description | Default |
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| --------------------- | --------------------------------------------- | ------------------- |
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| `--gene <symbol>` | Gene symbol to look up in RefSeq (e.g. `F12`) | |
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| `--taxon <name\|id>` | Taxon for `--gene` | `human` |
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| `--gene-id <id>` | NCBI GeneID, instead of `--gene` | |
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| `--transcript <acc>` | Specific transcript accession | MANE/RefSeq Select |
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| `--ref <rowname>` | Reference row = the transcript's CDS | first row |
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| `-o, --output <file>` | Output GFF file path | `genestructure.gff` |
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```bash
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# F12 coding alignment -> 14-exon overlay (MANE Select transcript, human row)
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react-msaview-cli genestructure f12-cds.stock --gene F12 --ref human -o exons.gff
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# pin a specific transcript
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react-msaview-cli genestructure aln.fa --transcript NM_000505.4 --ref human
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```
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## Examples
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### Using EBI API (recommended for small datasets)
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package/package.json
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{
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"name": "react-msaview-cli",
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"version": "5.
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"version": "5.5.0",
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"license": "MIT",
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"type": "module",
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"repository": {
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"dist"
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],
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"devDependencies": {
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"@types/jsdom": "^
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"@types/node": "^
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"@types/jsdom": "^28.0.3",
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"@types/node": "^26.0.1"
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},
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"dependencies": {
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"@emotion/react": "^11.14.0",
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"@emotion/styled": "^11.14.1",
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"@jbrowse/core": "^4.3.0",
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"@mui/material": "^7.3.11",
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"jsdom": "^
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"jsdom": "^29.1.1",
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"mobx": "^6.16.1",
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"mobx-react": "^9.2.2",
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"react": "^19.2.7",
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"react-dom": "^19.2.7",
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"msa-parsers": "5.
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"react-msaview": "5.
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"msa-parsers": "5.5.0",
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"react-msaview": "5.5.0"
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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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