react-msaview-cli 5.4.1 → 5.6.0

package/README.md

@@ -3,7 +3,9 @@
 Command-line tools for [react-msaview](../) (JBrowseMSA), including batch
 InterProScan processing for multiple sequence alignments.
 
-Uses [msa-parsers](../msa-parsers/) for file format support.
+Uses
+[msa-parsers](https://github.com/GMOD/JBrowseMSA/tree/main/packages/msa-parsers)
+for file format support.
 
 ## Installation
 
@@ -45,7 +47,7 @@ REST API one at a time. `--local`, `--docker`, and `--singularity` instead run
 InterProScan on the whole alignment locally, which is much faster for large
 datasets.
 
-#### Supported MSA Formats
+#### Supported MSA formats
 
 The CLI automatically detects the input format:
 
@@ -55,7 +57,7 @@ The CLI automatically detects the input format:
 - **A3M** (`.a3m`) - AlphaFold/ColabFold format
 - **EMF** (`.emf`) - Ensembl Multi Format
 
-#### Available InterProScan Programs
+#### Available InterProScan programs
 
 When using `--programs`, you can specify any combination of:
 
@@ -73,21 +75,117 @@ When using `--programs`, you can specify any combination of:
 - `PIRSF` - PIR SuperFamily
 - `MobiDBLite` - Disorder prediction
 
+### interpro
+
+Build a domain GFF from InterPro's **precomputed** matches for UniProtKB
+accessions, instead of submitting sequences to a live InterProScan job. Every
+UniProtKB sequence already has InterPro matches computed and served by the EBI
+InterPro API, so for inputs that are real UniProt accessions this is instant,
+deterministic, and version-pinnable — no email or rate-limited job submission.
+Prefer this over `interproscan` whenever your rows are UniProt accessions.
+
+```bash
+react-msaview-cli interpro <accessions.tsv> [options]
+```
+
+The input is one accession per line, optionally followed by a tab- or
+space-separated row label; lines starting with `#` are ignored. The output GFF
+is byte-for-byte compatible with the `interproscan` command.
+
+#### Options
+
+| Option                | Description                | Default       |
+| --------------------- | -------------------------- | ------------- |
+| `-o, --output <file>` | Output GFF file path       | `domains.gff` |
+| `--database <name>`   | InterPro member db to read | `pfam`        |
+
+```bash
+react-msaview-cli interpro accessions.tsv -o domains.gff
+react-msaview-cli interpro accessions.tsv -o domains.gff --database cdd
+```
+
+### genestructure
+
+Build a **gene-structure GFF** for a coding-sequence alignment from a RefSeq
+transcript, overlaid in react-msaview the same way InterProScan domains are. The
+exon model is fetched from the NCBI Datasets v2 API; each species' Nth exon is
+named `exon-N`, so a given exon is the same color in every row and the exon
+architecture reads straight down the alignment.
+
+```bash
+react-msaview-cli genestructure <input-msa> --gene <symbol> --ref <rowname> [options]
+```
+
+The exon boundaries of the chosen transcript are mapped onto the reference row's
+columns, then projected into every other row's own ungapped coordinates — so an
+exon that picks up a frameshifting indel in one lineage gets shorter on exactly
+that row while staying column-aligned with the rest. The reference row must be
+the transcript's coding sequence (the CLI warns if its length doesn't match).
+
+#### Options
+
+| Option                | Description                                   | Default             |
+| --------------------- | --------------------------------------------- | ------------------- |
+| `--gene <symbol>`     | Gene symbol to look up in RefSeq (e.g. `F12`) |                     |
+| `--taxon <name\|id>`  | Taxon for `--gene`                            | `human`             |
+| `--gene-id <id>`      | NCBI GeneID, instead of `--gene`              |                     |
+| `--transcript <acc>`  | Specific transcript accession                 | MANE/RefSeq Select  |
+| `--ref <rowname>`     | Reference row = the transcript's CDS          | first row           |
+| `-o, --output <file>` | Output GFF file path                          | `genestructure.gff` |
+
+```bash
+# F12 coding alignment -> 14-exon overlay (MANE Select transcript, human row)
+react-msaview-cli genestructure f12-cds.stock --gene F12 --ref human -o exons.gff
+
+# pin a specific transcript
+react-msaview-cli genestructure aln.fa --transcript NM_000505.4 --ref human
+```
+
+### export-svg
+
+Render an alignment (with an optional tree and domain overlay) straight to a
+standalone SVG — no browser required. This is what the R package shells out to
+for vector export.
+
+```bash
+react-msaview-cli export-svg --msa <file> [options]
+```
+
+#### Options
+
+| Option                   | Description                             | Default         |
+| ------------------------ | --------------------------------------- | --------------- |
+| `--msa <file>`           | MSA file (FASTA, Stockholm, or Clustal) | _required_      |
+| `--tree <file>`          | Newick tree file                        |                 |
+| `--gff <file>`           | InterProScan domain GFF file            |                 |
+| `-o, --output <file>`    | Output SVG file path                    | `alignment.svg` |
+| `--color-scheme <name>`  | Color scheme                            | `maeditor`      |
+| `--width <px>`           | Canvas width in pixels                  | `1200`          |
+| `--height <px>`          | Canvas height in pixels                 | `600`           |
+| `--tree-area-width <px>` | Tree panel width in pixels              |                 |
+
+```bash
+react-msaview-cli export-svg --msa alignment.fasta -o alignment.svg
+react-msaview-cli export-svg --msa alignment.fasta --tree tree.nwk -o alignment.svg
+react-msaview-cli export-svg --msa alignment.fasta --gff domains.gff \
+  --color-scheme clustalx_protein_dynamic -o alignment.svg
+```
+
 ## Examples
 
-### Using EBI API (recommended for small datasets)
+### Using the EBI API (recommended for small datasets)
 
 ```bash
-# Basic usage - runs Pfam analysis
+# Basic usage - runs the default PfamA + CDD analysis
 react-msaview-cli interproscan alignment.fasta -o domains.gff --email your@email.com
 
 # Multiple programs
 react-msaview-cli interproscan alignment.fasta -o domains.gff \
-  --programs Pfam,SMART,Gene3D \
+  --programs PfamA,SMART,Gene3D \
   --email your@email.com
 ```
 
-### Using Local InterProScan
+### Using local InterProScan
 
 For large datasets or frequent usage, install InterProScan locally:
 
@@ -103,7 +201,7 @@ react-msaview-cli interproscan alignment.fasta -o domains.gff \
 # With specific programs
 react-msaview-cli interproscan alignment.fasta -o domains.gff \
   --local \
-  --programs Pfam,SMART
+  --programs PfamA,SMART
 ```
 
 ### Using Docker
@@ -131,7 +229,7 @@ react-msaview-cli interproscan alignment.fasta -o domains.gff \
   --singularity-image /path/to/interproscan.sif
 ```
 
-### Different Input Formats
+### Different input formats
 
 ```bash
 # Clustal format
@@ -159,7 +257,7 @@ Writing output to domains.gff...
 Done!
 ```
 
-## Output Format
+## Output format
 
 The output is standard GFF3, with one `protein_match` line per domain hit.
 `start`/`end` are 1-based positions in the **ungapped** sequence (gaps are
@@ -173,7 +271,7 @@ seq1	InterProScan	protein_match	200	350	.	.	.	Name=PF00002;signature_desc=7tm_2;
 seq2	InterProScan	protein_match	5	120	.	.	.	Name=PF00001;signature_desc=7tm_1;description=7 transmembrane receptor (rhodopsin family)
 ```
 
-## Loading Results in react-msaview
+## Loading results in react-msaview
 
 After generating the GFF file, you can load it in react-msaview:
 
@@ -194,13 +292,13 @@ From R, pass the file (or string) as the `gff` argument:
 msaview(msa = "alignment.fasta", gff = "domains.gff")
 ```
 
-The domains render as labelled boxes over the matching rows:
+The domains render as labeled boxes over the matching rows:
 
 ![InterProScan domains rendered over an alignment](../../docs/media/example-domains.svg)
 
 ## Troubleshooting
 
-### EBI API Timeout
+### EBI API timeout
 
 If you get timeout errors with the EBI API:
 
@@ -208,7 +306,7 @@ If you get timeout errors with the EBI API:
 - Check your internet connection
 - For large datasets, a local/container backend is much faster than the API
 
-### Local InterProScan Not Found
+### Local InterProScan not found
 
 ```
 Error: Failed to run Local: spawn interproscan.sh ENOENT. Is interproscan.sh installed and on PATH?
@@ -220,13 +318,13 @@ Make sure InterProScan is installed and specify the full path:
 --interproscan-path /full/path/to/interproscan-5.xx/interproscan.sh
 ```
 
-### No Results in Output
+### No results in output
 
 - Check that your sequences are protein sequences (not nucleotide)
 - Try different programs (some may not have hits for your sequences)
 - Verify the input file is valid MSA format
 
-## API Rate Limits
+## API rate limits
 
 The EBI InterProScan API has usage limits:
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "react-msaview-cli",
-  "version": "5.4.1",
+  "version": "5.6.0",
   "license": "MIT",
   "type": "module",
   "repository": {
@@ -15,21 +15,21 @@
     "dist"
   ],
   "devDependencies": {
-    "@types/jsdom": "^21.1.7",
-    "@types/node": "^25.9.4"
+    "@types/jsdom": "^28.0.3",
+    "@types/node": "^26.1.1"
   },
   "dependencies": {
     "@emotion/react": "^11.14.0",
     "@emotion/styled": "^11.14.1",
-    "@jbrowse/core": "^4.3.0",
-    "@mui/material": "^7.3.11",
-    "jsdom": "^26.1.0",
+    "@jbrowse/core": "file:../../vendor-jbrowse/jbrowse-core.tgz",
+    "@mui/material": "^9.2.0",
+    "jsdom": "^29.1.1",
     "mobx": "^6.16.1",
     "mobx-react": "^9.2.2",
     "react": "^19.2.7",
     "react-dom": "^19.2.7",
-    "msa-parsers": "5.4.1",
-    "react-msaview": "5.4.1"
+    "msa-parsers": "5.6.0",
+    "react-msaview": "5.6.0"
   },
   "scripts": {
     "clean": "node --eval \"fs.rmSync('dist',{recursive:true,force:true})\" --input-type=module",