react-msaview-cli 6.5.0 → 8.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +161 -122
- package/dist/index.js +130746 -0
- package/package.json +12 -17
package/README.md
CHANGED
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Annotate a multiple sequence alignment and render it to a publication figure,
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from the command line, with no browser in the loop.
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The CLI has two groups of commands, and the second draws what the first writes:
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- **Annotate
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- **Annotate**: build a domain or exon GFF for an alignment, from InterPro's
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precomputed matches (`interpro`), a live InterProScan run (`interproscan`), or
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a RefSeq transcript's exon model (`genestructure`).
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- **Render
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standalone SVG (`export-svg`).
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- **Render**: draw the alignment, its tree, and those annotations to a
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standalone SVG (`export-svg`). The command runs the web viewer's renderer
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headlessly, so the figure matches what the app shows.
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## Prerequisites
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- NodeJS v22+
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scan with
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`export-svg` and `interpro` need nothing else. `interproscan` needs a backend to
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scan with: the EBI web API (the default, no install), Docker, Singularity, or a
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local InterProScan (see [interproscan](#interproscan)).
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`export-svg` draws the alignment background as one embedded image when
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[@napi-rs/canvas](https://www.npmjs.com/package/@napi-rs/canvas) is present.
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is an optional dependency with prebuilt binaries, so a normal install
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in
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rectangle per cell
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[@napi-rs/canvas](https://www.npmjs.com/package/@napi-rs/canvas) is present. The
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package is an optional dependency with prebuilt binaries, so a normal install
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brings it in. On a platform with no prebuilt binary, the export draws a
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rectangle per cell, which makes a much larger file and runs slower on big
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alignments.
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## Setup
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The domain architecture reads straight down the alignment
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the catalytic domain
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space
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The domain architecture reads straight down the alignment: SH3, then SH2, then
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the catalytic domain. The renderer draws every row in the alignment's column
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space, so each domain lands in the same columns in every row. The key on the
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right lists the domains present in the GFF.
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Every figure on this page is `export-svg` output, drawn from the Src-kinase and
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GPCR examples in
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[packages/examples](https://github.com/GMOD/JBrowseMSA/tree/main/packages/examples/
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[packages/examples](https://github.com/GMOD/JBrowseMSA/tree/main/packages/examples/data).
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## Rendering figures
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react-msaview-cli export-svg --msa <file> [options]
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```
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| Option | Description
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| ------------------------ |
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| `--msa <file>` | MSA file (FASTA, Stockholm, Clustal, A3M)
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| `--tree <file>` | Newick tree file
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| `--gff <file>` | Domain or exon GFF (from the commands below)
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| `-o, --output <file>` | Output SVG file path
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| `--color-scheme <name>` | Color scheme
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| `--col-width <px>` | Width of one alignment column
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| `--row-height <px>` | Height of one alignment row
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| `--width <px>` | Viewport width, which sets the tree area
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| `--height <px>` | Viewport height
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| `--tree-area-width <px>` | Tree panel width in pixels
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| Option | Description | Default |
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| ------------------------ | ---------------------------------------------- | --------------- |
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| `--msa <file>` | MSA file (FASTA, Stockholm, Clustal, A3M, EMF) | _required_ |
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| `--tree <file>` | Newick tree file | |
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| `--gff <file>` | Domain or exon GFF (from the commands below) | |
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| `-o, --output <file>` | Output SVG file path | `alignment.svg` |
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| `--color-scheme <name>` | Color scheme | `maeditor` |
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| `--col-width <px>` | Width of one alignment column | `12` |
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| `--row-height <px>` | Height of one alignment row | `16` |
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| `--width <px>` | Viewport width, which sets the tree area | `1200` |
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| `--height <px>` | Viewport height | `600` |
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| `--tree-area-width <px>` | Tree panel width in pixels | |
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| `--format <name>` | Force the MSA format instead of sniffing it | |
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| `--tracks <list>` | Tracks to draw above the alignment, by id | none |
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| `--viewport` | Draw the viewport instead of the whole thing | |
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| `--minimap` | Include the minimap bar (`--viewport` only) | |
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### Tracks
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`--tracks` names the tracks to draw above the alignment, by id, or `all` for
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every one this alignment has: `conservation`, `property-conservation` (protein
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only), `sequence-logo`, `position-ruler`, `base-pairs` (a Stockholm `SS_cons`
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line), and any track ids the file itself carries. The CLI reports a name that
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matches no track.
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```bash
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react-msaview-cli export-svg --msa kinases.aln --tracks conservation,position-ruler \
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-o kinases.svg
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```
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### Sizing the figure
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`export-svg`
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`--row-height
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`export-svg` draws the **entire** alignment unless `--viewport` asks for the
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`--width` x `--height` window at the top left, so the output is normally as wide
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as the alignment is long. `--width` and `--height` size the viewport the model
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lays out in, not the figure. `--col-width` and `--row-height` scale the figure:
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```bash
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## a 90-column alignment at the default 12px columns: letters are legible
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Residue letters draw only
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would be unreadable ink.
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Residue letters draw only in columns at least 5px wide and wider than half the
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row height, and in rows at least 8px tall. The app applies the same rule as you
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zoom out. Below that size the figure is the colored overview above, which
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usually suits a whole-alignment figure: at that scale the conserved blocks and
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gaps are visible, and letters would be too small to read.
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### Color schemes
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`cinema`, and the `jalview_*` family (`jalview_zappo`, `jalview_taylor`,
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`jalview_hydrophobicity`, `jalview_buried`, `jalview_prophelix`,
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`jalview_propstrand`, `jalview_propturn`) color each residue by identity. The
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two `_dynamic` schemes
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`percent_identity_dynamic
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`none` turns background color off.
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two `_dynamic` schemes, `clustalx_protein_dynamic` and
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`percent_identity_dynamic`, color each residue by the composition of its column,
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so conserved columns stand out by color. `nucleotide`, `clustalx_dna`,
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`jbrowse_dna` and `rainbow_dna` are for DNA; `none` turns background color off.
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### Output
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The SVG
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The SVG grows with the alignment: a 10-row by 856-column figure is about 700KB.
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The background is one embedded image where @napi-rs/canvas is installed, and a
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rectangle per cell where it is not. The letters, the tree and the annotations
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are vector either way. To convert to PNG or PDF for a journal:
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```bash
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rsvg-convert -w 2000 alignment.svg -o alignment.png
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inkscape alignment.svg --export-filename=alignment.pdf
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```
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be regenerated in CI and diffed.
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The same input gives the same bytes, so CI can regenerate a figure and diff it.
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## Annotating
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### interpro
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Build a domain GFF from InterPro's **precomputed** matches for UniProtKB
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accessions
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InterPro
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Prefer this over `interproscan` whenever your rows are UniProt accessions.
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accessions. The EBI InterPro API already serves matches for every UniProtKB
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sequence, so the lookup returns in seconds, gives the same result for a given
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InterPro release, and needs no email or rate-limited job. Use this instead of
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`interproscan` whenever your rows are UniProt accessions.
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```bash
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react-msaview-cli interpro <accessions.tsv> [options]
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```
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The input is one accession per line, optionally followed by a tab- or
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space-separated row label
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| `--
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space-separated row label. The command skips lines starting with `#`. It writes
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through the same GFF writer as `interproscan`, and adds a `#` header line naming
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the InterPro release the coordinates came from.
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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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| `--msa <file>` | Alignment to check the rows of (see below) | |
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| `--format <name>` | Force the `--msa` format instead of sniffing it | |
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| `--no-cache` | Re-fetch, ignoring the disk cache | off |
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InterPro computes matches on UniProt's canonical sequence, so on a row that is
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an isoform or a fragment the matches land on the wrong residues. With `--msa`,
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the CLI compares each row's ungapped length against the protein's and warns
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about any that differ. It also warns about any accession with no matches.
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```bash
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react-msaview-cli interpro accessions.tsv -o domains.gff
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#### Caching
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The InterPro API serves one protein per request
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with no matches are cached too, so they are not re-fetched every run.
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The InterPro API serves one protein per request and has no batch endpoint, so a
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run makes one request per distinct accession. The CLI caches every response on
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disk under `$XDG_CACHE_HOME/react-msaview-cli/interpro` (override with
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`REACT_MSAVIEW_CACHE`), keyed by InterPro release, so a new release fetches
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fresh coordinates. The cache also records proteins with no matches, so a re-run
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does not fetch them again.
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A re-run of the same dataset
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asking EBI for all of them again.
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A re-run of the same dataset makes one request, the release lookup, and reads
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the rest from disk. A failed run can therefore resume. The CLI retries with
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backoff, and if the API stays unreachable, the accessions it already fetched
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stay cached, so the next run fetches only the rest.
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### interproscan
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Run InterProScan on all sequences in an MSA file and output results as GFF3. Use
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this when the rows are not UniProt accessions
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proteins, anything InterPro has not
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this when the rows are not UniProt accessions: a de novo assembly, predicted
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proteins, or anything else InterPro has not scanned.
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```bash
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react-msaview-cli interproscan <input-msa> [options]
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```
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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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| `--local` | Use a local InterProScan installation instead of EBI | `false`
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| `--docker` | Run InterProScan via the `interpro/interproscan` image | `false`
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| `--singularity` | Run InterProScan via a Singularity/Apptainer container | `false`
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| `--
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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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| `--local` | Use a local InterProScan installation instead of EBI | `false` |
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| `--docker` | Run InterProScan via the `interpro/interproscan` image | `false` |
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| `--singularity` | Run InterProScan via a Singularity/Apptainer container | `false` |
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| `--docker-image <img>` | Docker image to run | `interpro/interproscan:5.78-109.0` |
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| `--singularity-image <img>` | Singularity image to use | `docker://interpro/interproscan:5.78-109.0` |
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| `--interproscan-path <path>` | Path to local interproscan.sh | `interproscan.sh` |
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| `--interproscan-data <dir>` | Member database `data/` to mount into the container | |
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| `--programs <list>` | Comma-separated list of programs, in EBI API naming | `PfamA,CDD` |
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| `--format <name>` | Force the MSA format instead of sniffing it | |
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| `--email <email>` | Email for EBI API (used only for EBI API runs) | `user@example.com` |
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By default (no backend flag) the CLI submits sequences to the EBI InterProScan
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REST API one at a time. `--local`, `--docker`, and `--singularity`
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REST API one at a time. `--local`, `--docker`, and `--singularity` run
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InterProScan on the whole alignment locally, which is much faster for large
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datasets.
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#### Choosing a backend
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```bash
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## EBI web API
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## EBI web API: no install, one sequential submission per sequence
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react-msaview-cli interproscan alignment.fasta -o domains.gff --email you@example.com
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## Docker
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## Docker: no InterProScan install, whole alignment in one run
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## a local install
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Docker mounts a temp directory into the `interpro/interproscan` container, runs
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the scan on the whole alignment at once, and reads the JSON back out.
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The
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which is a separate multi-gigabyte download. Fetch and unpack the matching
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release's `data/` directory (see the
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[InterProScan docs](https://interproscan-docs.readthedocs.io/)) and point
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`--interproscan-data` at it. Both container backends mount it at
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`/opt/interproscan/data` and look for it there.
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The EBI API has usage limits, so the CLI submits sequences one at a time. Past
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about 100 sequences, use a local or container backend.
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#### InterProScan programs
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`--programs` takes
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default), `SMART`, `
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`
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`--programs` takes the EBI API's names whichever backend runs: `PfamA` and `CDD`
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(the default), `SMART`, `SuperFamily`, `Gene3d`, `PANTHER`, `TIGRFAM`, `HAMAP`,
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`PrositeProfiles`, `PrositePatterns`, `PRINTS`, `PIRSF`, `MobiDBLite`, `Coils`,
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`SFLD`. InterProScan 5 spells several of them differently (`Pfam`, not `PfamA`;
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`NCBIfam`, which absorbed TIGRFAM; `Hamap`; `SUPERFAMILY`; `Gene3D`), and the
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CLI passes the translated names to the local, Docker and Singularity backends.
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```bash
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react-msaview-cli interproscan alignment.fasta -o domains.gff \
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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 the same way InterProScan domains are. The
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so a given exon is the same color in every row and the exon
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straight down the alignment.
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transcript, overlaid the same way InterProScan domains are. The command fetches
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the exon model from the NCBI Datasets v2 API and names each species' Nth exon
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`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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columns, then
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exon that picks up a frameshifting indel in one lineage gets
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that row
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the transcript's coding sequence
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The command maps the chosen transcript's exon boundaries onto the reference
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row's columns, then projects them into every other row's ungapped coordinates.
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An exon that picks up a frameshifting indel in one lineage therefore gets
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shorter on that row and stays in the same columns as the rest. The reference row
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must be the transcript's coding sequence; the CLI warns if its length doesn't
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match.
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| Option | Description | Default |
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| --------------------- | --------------------------------------------- | ------------------- |
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## Input formats
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The CLI
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The CLI sniffs the format from the file's content, not from its name. `--format`
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(`fasta`, `a3m`, `stockholm`, `clustal`, `emf`) overrides a wrong guess. FASTA
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and A3M share a leading `>`, so the CLI tells them apart heuristically.
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- **FASTA** (`.fasta`, `.fa`, `.faa`)
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- **Clustal** (`.clustal`, `.aln`)
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- **Stockholm** (`.sto`, `.stockholm`)
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- **A3M** (`.a3m`)
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- **EMF** (`.emf`)
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- **A3M** (`.a3m`), from AlphaFold/ColabFold
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- **EMF** (`.emf`), Ensembl Multi Format
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## Annotation output format
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The annotation commands write standard GFF3, one
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`
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-
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name, and
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The annotation commands write standard GFF3, one line per feature:
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`protein_match` for a domain from `interpro`/`interproscan`, `exon` for a
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segment from `genestructure`. `start`/`end` are 1-based positions in the
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**ungapped** sequence, and the attributes carry the accession, name, and
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description:
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```gff
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##gff-version 3
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Reading MSA from gpcrs.fasta...
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Found 4 sequences
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Processing 4 non-empty sequences...
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Running InterProScan via Docker...
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-
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docker run --rm -v /tmp/interproscan-Xyz12:/data interpro/interproscan:latest -i /data/input.fasta -o /data/output.json -f JSON -appl PfamA,CDD
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Running InterProScan via Docker on 4 sequences...
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docker run --rm -v /tmp/interproscan-Xyz12:/data -v /opt/interproscan-5.78-109.0/data:/opt/interproscan/data interpro/interproscan:5.78-109.0 -i /data/input.fasta -o /data/output.json -f JSON -appl Pfam,CDD
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Converting results to GFF...
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Writing output to domains.gff...
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Done!
|
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@@ -328,12 +365,12 @@ Done!
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## Using the GFF elsewhere
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The
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The web viewer, the React component and the R package all load the file the CLI
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writes.
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In the web viewer, select it in the import form's **Annotation GFF file or URL**
|
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field
|
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above.)
|
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|
+
field, or open it over a loaded alignment with **Annotations > Open annotation
|
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+
file...**, which also accepts the JSON an InterProScan run returns.
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In the React component, pass it inline as the `gff` prop:
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@@ -349,9 +386,10 @@ msaview(msa = "alignment.fasta", gff = "domains.gff")
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## Troubleshooting
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|
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**EBI API timeout.**
|
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-
|
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|
-
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|
+
**EBI API timeout.** We measured one sequence waiting fifteen minutes in the
|
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+
queue. The CLI waits an hour per job and keeps the results of the sequences that
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|
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+
finished. Use `--local`, `--docker`, or `--singularity` to run InterProScan
|
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|
+
yourself; on large datasets they are much faster than the API.
|
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|
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|
**Local InterProScan not found.**
|
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|
@@ -367,8 +405,9 @@ nucleotide; try other `--programs`; verify the input parses as one of the
|
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formats above.
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|
|
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**The exported figure is enormous.** `export-svg` draws the whole alignment at
|
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|
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`--col-width` per column.
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|
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residue letters stop drawing,
|
|
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|
+
`--col-width` per column. Lower `--col-width` until it fits. Below 5px, or below
|
|
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|
+
half the row height, the residue letters stop drawing, and they account for most
|
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|
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of the file size.
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## Uses
|
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