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react-msaview-cli\n\nAnnotate a multiple sequence alignment and render it to a publication figure,\nfrom the command line, with no browser in the loop.\n\nThe CLI has two groups of commands, and the second draws what the first writes:\n\n- **Annotate**: build a domain or exon GFF for an alignment, from InterPro's\n  precomputed matches (`interpro`), a live InterProScan run (`interproscan`), or\n  a RefSeq transcript's exon model (`genestructure`), and relate rows to 3D\n  structures (`residue-mappings`).\n- **Render**: draw the alignment, its tree, and those annotations to a\n  standalone SVG (`export-svg`). The command runs the web viewer's renderer\n  headlessly, so the figure matches what the app shows.\n\n## Prerequisites\n\n- NodeJS v22+\n\n`export-svg`, `interpro` and `residue-mappings` need nothing else.\n`interproscan` needs a backend to scan with: the EBI web API (the default, no\ninstall), Docker, Singularity, or a local InterProScan (see\n[interproscan](#interproscan)).\n\n`export-svg` draws the alignment background as one embedded image when\n[@napi-rs/canvas](https://www.npmjs.com/package/@napi-rs/canvas) is present. The\npackage is an optional dependency with prebuilt binaries, so a normal install\nbrings it in. On a platform with no prebuilt binary, the export draws a\nrectangle per cell, which makes a much larger file and runs slower on big\nalignments.\n\n## Setup\n\n```bash\nnpm install -g react-msaview-cli\n```\n\nFrom a clone of the monorepo instead:\n\n```bash\npnpm install\npnpm --filter react-msaview-cli build\n```\n\n## Quickstart\n\nAn Src-family kinase alignment with its tree and Pfam domains, rendered in two\ncommands. The first asks InterPro for the domains of each row; the second draws\nthe figure.\n\n```bash\nreact-msaview-cli interpro accessions.tsv -o domains.gff\n\nreact-msaview-cli export-svg --msa kinases.aln --tree kinases.nwk \\\n  --gff domains.gff --col-width 1.6 --row-height 14 --tree-area-width 200 \\\n  -o kinases.svg\n```\n\n![Src-family kinases: tree, SH3/SH2/kinase domain architecture, and the color key](../../docs/media/cli-domains.png)\n\nThe domain architecture reads straight down the alignment: SH3, then SH2, then\nthe catalytic domain. The renderer draws every row in the alignment's column\nspace, so each domain lands in the same columns in every row. The key on the\nright lists the domains present in the GFF.\n\nEvery figure on this page is `export-svg` output, drawn from the Src-kinase and\nGPCR examples in\n[packages/examples](https://github.com/GMOD/JBrowseMSA/tree/main/packages/examples/data).\n\n## Rendering figures\n\n```bash\nreact-msaview-cli export-svg --msa <file> [options]\n```\n\n| Option                   | Description                                    | Default         |\n| ------------------------ | ---------------------------------------------- | --------------- |\n| `--spec <file.json>`     | View spec or snapshot (see below)              |                 |\n| `--msa <file>`           | MSA file (FASTA, Stockholm, Clustal, A3M, EMF) | _required_      |\n| `--tree <file>`          | Newick tree file                               |                 |\n| `--gff <file>`           | Domain or exon GFF, or InterProScan JSON       |                 |\n| `-o, --output <file>`    | Output SVG file path                           | `alignment.svg` |\n| `--color-scheme <name>`  | Color scheme                                   | `maeditor`      |\n| `--col-width <px>`       | Width of one alignment column                  | `12`            |\n| `--row-height <px>`      | Height of one alignment row                    | `16`            |\n| `--width <px>`           | Viewport width, which sets the tree area       | `1200`          |\n| `--height <px>`          | Viewport height                                | `600`           |\n| `--tree-area-width <px>` | Tree panel width in pixels                     |                 |\n| `--format <name>`        | Force the MSA format instead of sniffing it    |                 |\n| `--tracks <list>`        | Tracks to draw above the alignment, by id      | none            |\n| `--viewport`             | Draw the viewport instead of the whole thing   |                 |\n| `--minimap`              | Include the minimap bar (`--viewport` only)    |                 |\n\n### Tracks\n\n`--tracks` names the tracks to draw above the alignment, by id, or `all` for\nevery one this alignment has: `conservation`, `property-conservation` (protein\nonly), `sequence-logo`, `position-ruler`, `base-pairs` (a Stockholm `SS_cons`\nline), and any track ids the file itself carries. The CLI reports a name that\nmatches no track.\n\n```bash\nreact-msaview-cli export-svg --msa kinases.aln --tracks conservation,position-ruler \\\n  -o kinases.svg\n```\n\n### Layers\n\n`--spec` takes an `MsaView` snapshot or its shorthand as a JSON file, so any\nlayer in [the layers reference](https://gmod.org/JBrowseMSA/layers) draws in the\nfigure: column tracks, highlights, clades, row panels, encodings. A spec that\nsets `msa`, `tree`, or a filehandle's `uri` to a relative path reads it beside\nthe spec file, and an `http(s)` one fetches it. `--msa` is then optional, and\nevery flag given on the command line overrides the spec. The figure draws the\ntracks the app would show for the spec, unless `--tracks` names them.\n\n```bash\nreact-msaview-cli export-svg --spec p53-view.json -o p53.svg\n```\n\n### Sizing the figure\n\n`export-svg` draws the **entire** alignment unless `--viewport` asks for the\n`--width` x `--height` window at the top left, so the output is normally as wide\nas the alignment is long. `--width` and `--height` size the viewport the model\nlays out in, not the figure. `--col-width` and `--row-height` scale the figure:\n\n```bash\n## a 90-column alignment at the default 12px columns: letters are legible\nreact-msaview-cli export-svg --msa gpcrs.fa -o gpcrs.svg\n```\n\n![Four GPCR rows with residue letters and a Pfam domain box](../../docs/media/cli-letters.png)\n\n```bash\n## an 856-column alignment at 1.4px columns: an overview, no letters\nreact-msaview-cli export-svg --msa kinases.aln --tree kinases.nwk \\\n  --col-width 1.4 --row-height 16 --tree-area-width 280 -o overview.svg\n```\n\n![The same kinase family drawn as a colored overview beside its tree](../../docs/media/cli-quickstart.png)\n\nResidue letters draw only in columns at least 5px wide and wider than half the\nrow height, and in rows at least 8px tall. The app applies the same rule as you\nzoom out. Below that size the figure is the colored overview above, which\nusually suits a whole-alignment figure: at that scale the conserved blocks and\ngaps are visible, and letters would be too small to read.\n\n### Color schemes\n\n```bash\nreact-msaview-cli export-svg --msa gpcrs.fa \\\n  --color-scheme clustalx_protein_dynamic -o gpcrs.svg\n```\n\n![The same GPCR rows under the ClustalX scheme](../../docs/media/cli-clustalx.png)\n\n`maeditor` (the default), `clustal`, `clustalx_protein`, `lesk`, `flower`,\n`cinema`, and the `jalview_*` family (`jalview_zappo`, `jalview_taylor`,\n`jalview_hydrophobicity`, `jalview_buried`, `jalview_prophelix`,\n`jalview_propstrand`, `jalview_propturn`) color each residue by identity. The\ntwo `_dynamic` schemes, `clustalx_protein_dynamic` and\n`percent_identity_dynamic`, color each residue by the composition of its column,\nso conserved columns stand out by color. `nucleotide`, `clustalx_dna`,\n`jbrowse_dna` and `rainbow_dna` are for DNA; `none` turns background color off.\n\n### Output\n\nThe SVG grows with the alignment: a 10-row by 856-column figure is about 700KB.\nThe background is one embedded image where @napi-rs/canvas is installed, and a\nrectangle per cell where it is not. The letters, the tree and the annotations\nare vector either way. To convert to PNG or PDF for a journal:\n\n```bash\nrsvg-convert -w 2000 alignment.svg -o alignment.png\ninkscape alignment.svg --export-filename=alignment.pdf\n```\n\nThe same input gives the same bytes, so CI can regenerate a figure and diff it.\n\n## Annotating\n\n### interpro\n\nBuild a domain GFF from InterPro's **precomputed** matches for UniProtKB\naccessions. The EBI InterPro API already serves matches for every UniProtKB\nsequence, so the lookup returns in seconds, gives the same result for a given\nInterPro release, and needs no email or rate-limited job. Use this instead of\n`interproscan` whenever your rows are UniProt accessions.\n\n```bash\nreact-msaview-cli interpro <accessions.tsv> [options]\n```\n\nThe input is one accession per line, optionally followed by a tab- or\nspace-separated row label. The command skips lines starting with `#`. It reads\nan isoform (`P04637-2`) or versioned (`P04637.4`) accession as the canonical one\nand warns, and stops before any request on an entry name (`P53_HUMAN`), a RefSeq\nid or anything else InterPro does not key by; run `interproscan` on those. It\nwrites through the same GFF writer as `interproscan`, and adds a `#` header line\nnaming the InterPro release the coordinates came from.\n\n| Option                | Description                                     | Default       |\n| --------------------- | ----------------------------------------------- | ------------- |\n| `-o, --output <file>` | Output GFF file path                            | `domains.gff` |\n| `--database <name>`   | InterPro member db to read                      | `pfam`        |\n| `--msa <file>`        | Alignment to check the rows of (see below)      |               |\n| `--format <name>`     | Force the `--msa` format instead of sniffing it |               |\n| `--no-cache`          | Re-fetch, ignoring the disk cache               | off           |\n\nInterPro computes matches on UniProt's canonical sequence. A label ending in\n`/start-end`, as Pfam and Stockholm name a fragment row (`P12931/84-145`), moves\neach match into the fragment's own positions and clips it to the fragment. On an\nisoform row the matches land on the wrong residues. With `--msa`, the CLI\ncompares each row's ungapped length against the protein's, or against the\nrange's for a fragment, and warns about any that differ. It also warns about any\naccession with no matches.\n\n```bash\nreact-msaview-cli interpro accessions.tsv -o domains.gff\nreact-msaview-cli interpro accessions.tsv -o domains.gff --database cdd\n```\n\n#### Caching\n\nThe InterPro API serves one protein per request and has no batch endpoint, so a\nrun makes one request per distinct accession. The CLI caches every response on\ndisk under `$XDG_CACHE_HOME/react-msaview-cli/interpro` (override with\n`REACT_MSAVIEW_CACHE`), keyed by InterPro release, so a new release fetches\nfresh coordinates. The cache also records proteins with no matches, so a re-run\ndoes not fetch them again.\n\nA re-run of the same dataset makes one request, the release lookup, and reads\nthe rest from disk. A failed run can therefore resume. The CLI retries with\nbackoff, and if the API stays unreachable, the accessions it already fetched\nstay cached, so the next run fetches only the rest.\n\nWhen the release lookup fails, the CLI warns and reads the newest release in the\ncache, so a fully cached run needs no network.\n\n### interproscan\n\nRun InterProScan on all sequences in an MSA file and output results as GFF3. Use\nthis when the rows are not UniProt accessions: a de novo assembly, predicted\nproteins, or anything else InterPro has not scanned.\n\n```bash\nreact-msaview-cli interproscan <input-msa> [options]\n```\n\n| Option                       | Description                                            | Default                                     |\n| ---------------------------- | ------------------------------------------------------ | ------------------------------------------- |\n| `-o, --output <file>`        | Output GFF file path                                   | `domains.gff`                               |\n| `--local`                    | Use a local InterProScan installation instead of EBI   | `false`                                     |\n| `--docker`                   | Run InterProScan via the `interpro/interproscan` image | `false`                                     |\n| `--singularity`              | Run InterProScan via a Singularity/Apptainer container | `false`                                     |\n| `--docker-image <img>`       | Docker image to run                                    | `interpro/interproscan:5.78-109.0`          |\n| `--singularity-image <img>`  | Singularity image to use                               | `docker://interpro/interproscan:5.78-109.0` |\n| `--interproscan-path <path>` | Path to local interproscan.sh                          | `interproscan.sh`                           |\n| `--interproscan-data <dir>`  | Member database `data/` to mount into the container    |                                             |\n| `--programs <list>`          | Comma-separated list of programs, in EBI API naming    | `PfamA,CDD`                                 |\n| `--format <name>`            | Force the MSA format instead of sniffing it            |                                             |\n| `--email <email>`            | Email for EBI API (used only for EBI API runs)         | `user@example.com`                          |\n\nBy default (no backend flag) the CLI submits sequences to the EBI InterProScan\nREST API one at a time. `--local`, `--docker`, and `--singularity` run\nInterProScan on the whole alignment locally, which is much faster for large\ndatasets.\n\n#### Choosing a backend\n\n```bash\n## EBI web API: no install, one sequential submission per sequence\nreact-msaview-cli interproscan alignment.fasta -o domains.gff --email you@example.com\n\n## Docker: no InterProScan install, whole alignment in one run\nreact-msaview-cli interproscan alignment.fasta -o domains.gff --docker\n\n## a local install\nreact-msaview-cli interproscan alignment.fasta -o domains.gff \\\n  --local --interproscan-path /opt/interproscan/interproscan.sh\n\n## Singularity/Apptainer, for HPC clusters without Docker\nreact-msaview-cli interproscan alignment.fasta -o domains.gff \\\n  --singularity --singularity-image /path/to/interproscan.sif\n```\n\nDocker mounts a temp directory into the `interpro/interproscan` container, runs\nthe scan on the whole alignment at once, and reads the JSON back out.\n\nThe published image carries InterProScan but **not** its member database data,\nwhich is a separate multi-gigabyte download. Fetch and unpack the matching\nrelease's `data/` directory (see the\n[InterProScan docs](https://interproscan-docs.readthedocs.io/)) and point\n`--interproscan-data` at it. Both container backends mount it at\n`/opt/interproscan/data` and look for it there.\n\nThe EBI API has usage limits, so the CLI submits sequences one at a time. Past\nabout 100 sequences, use a local or container backend.\n\n#### InterProScan programs\n\n`--programs` takes the EBI API's names whichever backend runs: `PfamA` and `CDD`\n(the default), `SMART`, `SuperFamily`, `Gene3d`, `PANTHER`, `TIGRFAM`, `HAMAP`,\n`PrositeProfiles`, `PrositePatterns`, `PRINTS`, `PIRSF`, `MobiDBLite`, `Coils`,\n`SFLD`. InterProScan 5 spells several of them differently (`Pfam`, not `PfamA`;\n`NCBIfam`, which absorbed TIGRFAM; `Hamap`; `SUPERFAMILY`; `Gene3D`), and the\nCLI passes the translated names to the local, Docker and Singularity backends.\n\n```bash\nreact-msaview-cli interproscan alignment.fasta -o domains.gff \\\n  --programs PfamA,SMART,Gene3D --email you@example.com\n```\n\n### genestructure\n\nBuild a **gene-structure GFF** for a coding-sequence alignment from a RefSeq\ntranscript, overlaid the same way InterProScan domains are. The command fetches\nthe exon model from the NCBI Datasets v2 API and names each species' Nth exon\n`exon-N`, so a given exon is the same color in every row and the exon\narchitecture reads straight down the alignment.\n\n```bash\nreact-msaview-cli genestructure <input-msa> --gene <symbol> --ref <rowname> [options]\n```\n\nThe command maps the chosen transcript's exon boundaries onto the reference\nrow's columns, then projects them into every other row's ungapped coordinates.\nAn exon that picks up a frameshifting indel in one lineage therefore gets\nshorter on that row and stays in the same columns as the rest. The reference row\nmust be the transcript's coding sequence; the CLI warns if its length doesn't\nmatch.\n\n| Option                | Description                                   | Default             |\n| --------------------- | --------------------------------------------- | ------------------- |\n| `--gene <symbol>`     | Gene symbol to look up in RefSeq (e.g. `F12`) |                     |\n| `--taxon <name\\|id>`  | Taxon for `--gene`                            | `human`             |\n| `--gene-id <id>`      | NCBI GeneID, instead of `--gene`              |                     |\n| `--transcript <acc>`  | Specific transcript accession                 | MANE/RefSeq Select  |\n| `--ref <rowname>`     | Reference row = the transcript's CDS          | first row           |\n| `-o, --output <file>` | Output GFF file path                          | `genestructure.gff` |\n\n```bash\n## F12 coding alignment -> 14-exon overlay (MANE Select transcript, human row)\nreact-msaview-cli genestructure f12-cds.stock --gene F12 --ref human -o exons.gff\n\n## pin a specific transcript\nreact-msaview-cli genestructure aln.fa --transcript NM_000505.4 --ref human\n```\n\n### residue-mappings\n\nBuild the\n[`residueMappings` layer](https://github.com/GMOD/JBrowseMSA/blob/main/docs/layers.md#residuemappings),\nwhich tells the viewer which residue of a PDB chain or an AlphaFold model each\nresidue of a row is. The output is `{\"residueMappings\": [...]}`, ready for the\n`residueMappings` prop, a `#data=` link, or the R and Python widgets.\n\n```bash\nreact-msaview-cli residue-mappings --msa <file> --row <name> --accession <acc> \\\n  (--pdb <id> --chain <id> | --alphafold) [-o mappings.json]\nreact-msaview-cli residue-mappings --msa <file> --rows <tsv> [-o mappings.json]\n```\n\n| Option                    | Description                                             | Default |\n| ------------------------- | ------------------------------------------------------- | ------- |\n| `--msa <file>`            | Alignment holding the rows                              |         |\n| `--format <name>`         | Force the MSA format instead of sniffing it             |         |\n| `--rows <tsv>`            | `row`, `accession`, `structure` per line, tab-separated |         |\n| `--row <name>`            | One row, instead of `--rows`                            |         |\n| `--accession <acc>`       | The row's UniProtKB accession                           |         |\n| `--pdb <id> --chain <id>` | The PDB entry and its author chain                      |         |\n| `--alphafold`             | The AlphaFold DB model of the accession instead         |         |\n| `-o, --output <file>`     | Output JSON file                                        | stdout  |\n\nIn `--rows`, the structure column is `6VXX:A` or `alphafold`, and a\n`row accession structure` header line is optional. A row may appear on several\nlines to map it onto several structures.\n\nFor each row, the CLI first fetches the accession's sequence from UniProt and\nchecks the row's ungapped residues against it. A row named `/start-end` has to\nmatch that slice of the protein, and every position in its mapping is a residue\nof the row. A mismatch stops the run with the row, the accession and the first\nresidue where they differ.\n\nFor a PDB chain, the segments come from the PDBe SIFTS mapping of the entry, and\n`unobserved` lists every position of the chain's entity outside PDBe's observed\nranges. `asymId` is the `struct_asym_id` SIFTS gives for the author chain. For\nan AlphaFold model, the model numbers the protein from 1, so the mapping is one\nsegment and has no `unobserved`.\n\n```console\n$ react-msaview-cli residue-mappings --msa spike.afa --row SARS-CoV-2 \\\n    --accession P0DTC2 --pdb 6VXX --chain A -o mappings.json\n  SARS-CoV-2: P0DTC2 onto 6VXX chain A, row 14-1211 at 33-1230\nwrote mappings.json\n```\n\n## Input formats\n\nThe CLI sniffs the format from the file's content, not from its name. `--format`\n(`fasta`, `a3m`, `stockholm`, `clustal`, `emf`) overrides a wrong guess. FASTA\nand A3M share a leading `>`, so the CLI tells them apart heuristically.\n\n- **FASTA** (`.fasta`, `.fa`, `.faa`)\n- **Clustal** (`.clustal`, `.aln`)\n- **Stockholm** (`.sto`, `.stockholm`)\n- **A3M** (`.a3m`), from AlphaFold/ColabFold\n- **EMF** (`.emf`), Ensembl Multi Format\n\n## Annotation output format\n\nThe annotation commands write standard GFF3, one line per feature:\n`protein_match` for a domain from `interpro`/`interproscan`, `exon` for a\nsegment from `genestructure`. `start`/`end` are 1-based positions in the\n**ungapped** sequence, and the attributes carry the accession, name, and\ndescription:\n\n```gff\n##gff-version 3\nseq1\tInterProScan\tprotein_match\t10\t150\t.\t.\t.\tName=PF00001;signature_desc=7tm_1;description=7 transmembrane receptor (rhodopsin family)\nseq1\tInterProScan\tprotein_match\t200\t350\t.\t.\t.\tName=PF00002;signature_desc=7tm_2;description=7 transmembrane receptor (Secretin family)\nseq2\tInterProScan\tprotein_match\t5\t120\t.\t.\t.\tName=PF00001;signature_desc=7tm_1;description=7 transmembrane receptor (rhodopsin family)\n```\n\nA worked run:\n\n```console\n$ react-msaview-cli interproscan gpcrs.fasta -o domains.gff --docker\nReading MSA from gpcrs.fasta...\nFound 4 sequences\nProcessing 4 non-empty sequences...\n  Running InterProScan via Docker on 4 sequences...\n  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\nConverting results to GFF...\nWriting output to domains.gff...\nDone!\n```\n\n## Using the GFF elsewhere\n\nThe web viewer, the React component and the R package all load the file the CLI\nwrites.\n\nIn the web viewer, select it in the import form's **Annotation GFF file or URL**\nfield, or open it over a loaded alignment with **Annotations > Open annotation\nfile...**, which also accepts the JSON an InterProScan run returns.\n\nIn the React component, pass it inline as the `gff` prop:\n\n```jsx\n<MSAViewer msa={msaText} gff={domainsGff} />\n```\n\nFrom R:\n\n```r\nmsaview(msa = \"alignment.fasta\", gff = \"domains.gff\")\n```\n\n## Troubleshooting\n\n**EBI API timeout.** We measured one sequence waiting fifteen minutes in the\nqueue. The CLI waits an hour per job and keeps the results of the sequences that\nfinished. Use `--local`, `--docker`, or `--singularity` to run InterProScan\nyourself; on large datasets they are much faster than the API.\n\n**Local InterProScan not found.**\n\n```\nError: Failed to run Local: spawn interproscan.sh ENOENT. Is interproscan.sh installed and on PATH?\n```\n\nGive the full path:\n`--interproscan-path /full/path/to/interproscan-5.xx/interproscan.sh`\n\n**No results in the output.** Check that the sequences are protein, not\nnucleotide; try other `--programs`; verify the input parses as one of the\nformats above.\n\n**The exported figure is enormous.** `export-svg` draws the whole alignment at\n`--col-width` per column. Lower `--col-width` until it fits. Below 5px, or below\nhalf the row height, the residue letters stop drawing, and they account for most\nof the file size.\n\n## Uses\n\n[msa-parsers](https://github.com/GMOD/JBrowseMSA/tree/main/packages/msa-parsers)\nfor file format support, and\n[react-msaview](https://github.com/GMOD/JBrowseMSA/tree/main/packages/lib) for\nrendering.\n\n## License\n\nMIT\n","readmeFilename":""}