react-msaview-cli 8.3.0 → 8.4.0
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- package/README.md +7 -7
- package/dist/index.js +16821 -56755
- package/package.json +3 -3
package/README.md
CHANGED
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@@ -107,12 +107,12 @@ react-msaview-cli export-svg --msa kinases.aln --tracks conservation,position-ru
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### Layers
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`--spec` takes an `MsaView` snapshot or its shorthand as a JSON file, so any
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layer in [
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tracks, highlights, clades, row panels, encodings. A spec that
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`tree`, or a filehandle's `uri` to a relative path reads it beside
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file, and an `http(s)` one fetches it. `--msa` is then optional, and
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given on the command line overrides the spec. The figure draws the
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app would show for the spec, unless `--tracks` names them.
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layer in [the layers reference](https://gmod.org/JBrowseMSA/layers) draws in the
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figure: column tracks, highlights, clades, row panels, encodings. A spec that
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sets `msa`, `tree`, or a filehandle's `uri` to a relative path reads it beside
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the spec file, and an `http(s)` one fetches it. `--msa` is then optional, and
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every flag given on the command line overrides the spec. The figure draws the
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tracks the app would show for the spec, unless `--tracks` names them.
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```bash
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react-msaview-cli export-svg --spec p53-view.json -o p53.svg
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@@ -354,7 +354,7 @@ Build the
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[`residueMappings` layer](https://github.com/GMOD/JBrowseMSA/blob/main/docs/layers.md#residuemappings),
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which tells the viewer which residue of a PDB chain or an AlphaFold model each
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residue of a row is. The output is `{"residueMappings": [...]}`, ready for the
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`residueMappings` prop, a
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`residueMappings` prop, a `#data=` link, or the R and Python widgets.
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```bash
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react-msaview-cli residue-mappings --msa <file> --row <name> --accession <acc> \
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