react-msaview-cli 6.1.1 → 6.2.1

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  1. package/README.md +225 -210
  2. package/package.json +3 -3
package/README.md CHANGED
@@ -1,79 +1,144 @@
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1
  # react-msaview-cli
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2
 
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- Command-line tools for [react-msaview](../) (JBrowseMSA), including batch
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- InterProScan processing for multiple sequence alignments.
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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.
5
5
 
6
- Uses
7
- [msa-parsers](https://github.com/GMOD/JBrowseMSA/tree/main/packages/msa-parsers)
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- for file format support.
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+ Two things live here, and they compose:
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+
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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
10
+ a RefSeq transcript's exon model (`genestructure`).
11
+ - **Render** — draw the alignment, its tree, and those annotations to a
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+ standalone SVG (`export-svg`). This is the same renderer the web viewer uses,
13
+ driven headlessly, so the figure matches what the app shows.
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+
15
+ ## Prerequisites
9
16
 
10
- ## Installation
17
+ - NodeJS v22+
18
+
19
+ Nothing else for `export-svg` and `interpro`. `interproscan` needs a backend to
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+ scan with — the EBI web API (the default, no install), or Docker, Singularity,
21
+ or a local InterProScan (see [interproscan](#interproscan)).
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+
23
+ ## Setup
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+
25
+ ```bash
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+ npm install -g react-msaview-cli
27
+ ```
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+
29
+ From a clone of the monorepo instead:
11
30
 
12
31
  ```bash
13
- # From the monorepo root
14
32
  pnpm install
15
33
  pnpm --filter react-msaview-cli build
34
+ ```
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+
36
+ ## Quickstart
16
37
 
17
- # Or install globally (after publishing)
18
- pnpm add -g react-msaview-cli
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+ An Src-family kinase alignment with its tree and Pfam domains, rendered in two
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+ commands. The first asks InterPro for the domains of each row; the second draws
40
+ the figure.
41
+
42
+ ```bash
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+ react-msaview-cli interpro accessions.tsv -o domains.gff
44
+
45
+ react-msaview-cli export-svg --msa kinases.aln --tree kinases.nwk \
46
+ --gff domains.gff --col-width 1.6 --row-height 14 --tree-area-width 200 \
47
+ -o kinases.svg
19
48
  ```
20
49
 
21
- ## Commands
50
+ ![Src-family kinases: tree, SH3/SH2/kinase domain architecture, and the color key](../../docs/media/cli-domains.png)
22
51
 
23
- ### interproscan
52
+ The domain architecture reads straight down the alignment — SH3, then SH2, then
53
+ the catalytic domain — because every row is drawn in the alignment's own column
54
+ space. The key on the right is generated from the domains actually present.
24
55
 
25
- Run InterProScan on all sequences in an MSA file and output results as GFF3.
56
+ Every figure on this page is `export-svg` output, drawn from the Src-kinase and
57
+ GPCR examples in
58
+ [packages/examples](https://github.com/GMOD/JBrowseMSA/tree/main/packages/examples/src/examples/exampleData.ts).
59
+
60
+ ## Rendering figures
26
61
 
27
62
  ```bash
28
- react-msaview-cli interproscan <input-msa> [options]
63
+ react-msaview-cli export-svg --msa <file> [options]
29
64
  ```
30
65
 
31
- #### Options
66
+ | Option | Description | Default |
67
+ | ------------------------ | -------------------------------------------- | --------------- |
68
+ | `--msa <file>` | MSA file (FASTA, Stockholm, Clustal, A3M) | _required_ |
69
+ | `--tree <file>` | Newick tree file | |
70
+ | `--gff <file>` | Domain or exon GFF (from the commands below) | |
71
+ | `-o, --output <file>` | Output SVG file path | `alignment.svg` |
72
+ | `--color-scheme <name>` | Color scheme | `maeditor` |
73
+ | `--col-width <px>` | Width of one alignment column | `12` |
74
+ | `--row-height <px>` | Height of one alignment row | `16` |
75
+ | `--width <px>` | Viewport width, which sets the tree area | `1200` |
76
+ | `--height <px>` | Viewport height | `600` |
77
+ | `--tree-area-width <px>` | Tree panel width in pixels | |
78
+
79
+ ### Sizing the figure
80
+
81
+ `export-svg` always draws the **entire** alignment, so the output is as wide as
82
+ the alignment is long — `--width` and `--height` size the viewport the model
83
+ lays out in, not the figure. What scales the figure is `--col-width` and
84
+ `--row-height`:
32
85
 
33
- | Option | Description | Default |
34
- | ---------------------------- | ------------------------------------------------------ | --------------------------------------- |
35
- | `-o, --output <file>` | Output GFF file path | `domains.gff` |
36
- | `--local` | Use a local InterProScan installation instead of EBI | `false` |
37
- | `--docker` | Run InterProScan via the `interpro/interproscan` image | `false` |
38
- | `--singularity` | Run InterProScan via a Singularity/Apptainer container | `false` |
39
- | `--singularity-image <img>` | Singularity image to use | `docker://interpro/interproscan:latest` |
40
- | `--interproscan-path <path>` | Path to local interproscan.sh | `interproscan.sh` |
41
- | `--programs <list>` | Comma-separated list of InterProScan programs | `PfamA,CDD` |
42
- | `--email <email>` | Email for EBI API (used only for EBI API runs) | `user@example.com` |
43
- | `-h, --help` | Show help message | |
86
+ ```bash
87
+ ## a 90-column alignment at the default 12px columns: letters are legible
88
+ react-msaview-cli export-svg --msa gpcrs.fa -o gpcrs.svg
89
+ ```
44
90
 
45
- By default (no backend flag) the CLI submits sequences to the EBI InterProScan
46
- REST API one at a time. `--local`, `--docker`, and `--singularity` instead run
47
- InterProScan on the whole alignment locally, which is much faster for large
48
- datasets.
91
+ ![Four GPCR rows with residue letters and a Pfam domain box](../../docs/media/cli-letters.png)
92
+
93
+ ```bash
94
+ ## an 856-column alignment at 1.4px columns: an overview, no letters
95
+ react-msaview-cli export-svg --msa kinases.aln --tree kinases.nwk \
96
+ --col-width 1.4 --row-height 16 --tree-area-width 280 -o overview.svg
97
+ ```
49
98
 
50
- #### Supported MSA formats
99
+ ![The same kinase family drawn as a colored overview beside its tree](../../docs/media/cli-quickstart.png)
51
100
 
52
- The CLI automatically detects the input format:
101
+ Residue letters draw only where there is room for them — columns at least 5px
102
+ wide and wider than half the row height, rows at least 8px tall — which is the
103
+ same rule the app applies as you zoom out. Below that you get the colored
104
+ overview above, and for a whole-alignment figure that is usually what you want:
105
+ the conserved blocks and the gaps are the signal at that scale, and the letters
106
+ would be unreadable ink.
53
107
 
54
- - **FASTA** (`.fasta`, `.fa`, `.faa`)
55
- - **Clustal** (`.clustal`, `.aln`)
56
- - **Stockholm** (`.sto`, `.stockholm`)
57
- - **A3M** (`.a3m`) - AlphaFold/ColabFold format
58
- - **EMF** (`.emf`) - Ensembl Multi Format
59
-
60
- #### Available InterProScan programs
61
-
62
- When using `--programs`, you can specify any combination of:
63
-
64
- - `PfamA` - Protein families (part of the `PfamA,CDD` default)
65
- - `SMART` - Simple Modular Architecture Research Tool
66
- - `SUPERFAMILY` - Structural and functional annotation
67
- - `Gene3D` - Structural domain assignments
68
- - `CDD` - Conserved Domain Database
69
- - `PANTHER` - Protein Analysis Through Evolutionary Relationships
70
- - `TIGRFAM` - TIGR protein families
71
- - `Hamap` - High-quality Automated Annotation of Microbial Proteomes
72
- - `ProSiteProfiles` - PROSITE profiles
73
- - `ProSitePatterns` - PROSITE patterns
74
- - `PRINTS` - Protein fingerprints
75
- - `PIRSF` - PIR SuperFamily
76
- - `MobiDBLite` - Disorder prediction
108
+ ### Color schemes
109
+
110
+ ```bash
111
+ react-msaview-cli export-svg --msa gpcrs.fa \
112
+ --color-scheme clustalx_protein_dynamic -o gpcrs.svg
113
+ ```
114
+
115
+ ![The same GPCR rows under the ClustalX scheme](../../docs/media/cli-clustalx.png)
116
+
117
+ `maeditor` (the default), `clustal`, `clustalx_protein`, `lesk`, `flower`,
118
+ `cinema`, and the `jalview_*` family (`jalview_zappo`, `jalview_taylor`,
119
+ `jalview_hydrophobicity`, `jalview_buried`, `jalview_prophelix`,
120
+ `jalview_propstrand`, `jalview_propturn`) color each residue by identity. The
121
+ two `_dynamic` schemes — `clustalx_protein_dynamic` and
122
+ `percent_identity_dynamic` — color by what the column actually contains, so
123
+ conservation shows up as color rather than as something you have to read off.
124
+ `nucleotide`, `clustalx_dna`, `jbrowse_dna` and `rainbow_dna` are for DNA;
125
+ `none` turns background color off.
126
+
127
+ ### Output
128
+
129
+ The SVG is pure vector: every cell is its own rectangle, so it scales without
130
+ limit but grows with the alignment. A 10-row by 856-column figure is about
131
+ 700KB. Converting to PNG or PDF for a journal:
132
+
133
+ ```bash
134
+ rsvg-convert -w 2000 alignment.svg -o alignment.png
135
+ inkscape alignment.svg --export-filename=alignment.pdf
136
+ ```
137
+
138
+ Exports are reproducible — the same input gives the same bytes, so a figure can
139
+ be regenerated in CI and diffed.
140
+
141
+ ## Annotating
77
142
 
78
143
  ### interpro
79
144
 
@@ -92,8 +157,6 @@ The input is one accession per line, optionally followed by a tab- or
92
157
  space-separated row label; lines starting with `#` are ignored. The output GFF
93
158
  is byte-for-byte compatible with the `interproscan` command.
94
159
 
95
- #### Options
96
-
97
160
  | Option | Description | Default |
98
161
  | --------------------- | --------------------------------- | ------------- |
99
162
  | `-o, --output <file>` | Output GFF file path | `domains.gff` |
@@ -121,145 +184,128 @@ are automatic with backoff, and if the API is still unreachable the accessions
121
184
  already fetched stay cached, so re-running picks up where it stopped instead of
122
185
  asking EBI for all of them again.
123
186
 
124
- ### genestructure
187
+ ### interproscan
125
188
 
126
- Build a **gene-structure GFF** for a coding-sequence alignment from a RefSeq
127
- transcript, overlaid in react-msaview the same way InterProScan domains are. The
128
- exon model is fetched from the NCBI Datasets v2 API; each species' Nth exon is
129
- named `exon-N`, so a given exon is the same color in every row and the exon
130
- architecture reads straight down the alignment.
189
+ Run InterProScan on all sequences in an MSA file and output results as GFF3. Use
190
+ this when the rows are not UniProt accessions — a de novo assembly, predicted
191
+ proteins, anything InterPro has not already scanned.
131
192
 
132
193
  ```bash
133
- react-msaview-cli genestructure <input-msa> --gene <symbol> --ref <rowname> [options]
194
+ react-msaview-cli interproscan <input-msa> [options]
134
195
  ```
135
196
 
136
- The exon boundaries of the chosen transcript are mapped onto the reference row's
137
- columns, then projected into every other row's own ungapped coordinates — so an
138
- exon that picks up a frameshifting indel in one lineage gets shorter on exactly
139
- that row while staying column-aligned with the rest. The reference row must be
140
- the transcript's coding sequence (the CLI warns if its length doesn't match).
197
+ | Option | Description | Default |
198
+ | ---------------------------- | ------------------------------------------------------ | --------------------------------------- |
199
+ | `-o, --output <file>` | Output GFF file path | `domains.gff` |
200
+ | `--local` | Use a local InterProScan installation instead of EBI | `false` |
201
+ | `--docker` | Run InterProScan via the `interpro/interproscan` image | `false` |
202
+ | `--singularity` | Run InterProScan via a Singularity/Apptainer container | `false` |
203
+ | `--singularity-image <img>` | Singularity image to use | `docker://interpro/interproscan:latest` |
204
+ | `--interproscan-path <path>` | Path to local interproscan.sh | `interproscan.sh` |
205
+ | `--programs <list>` | Comma-separated list of InterProScan programs | `PfamA,CDD` |
206
+ | `--email <email>` | Email for EBI API (used only for EBI API runs) | `user@example.com` |
141
207
 
142
- #### Options
208
+ By default (no backend flag) the CLI submits sequences to the EBI InterProScan
209
+ REST API one at a time. `--local`, `--docker`, and `--singularity` instead run
210
+ InterProScan on the whole alignment locally, which is much faster for large
211
+ datasets.
143
212
 
144
- | Option | Description | Default |
145
- | --------------------- | --------------------------------------------- | ------------------- |
146
- | `--gene <symbol>` | Gene symbol to look up in RefSeq (e.g. `F12`) | |
147
- | `--taxon <name\|id>` | Taxon for `--gene` | `human` |
148
- | `--gene-id <id>` | NCBI GeneID, instead of `--gene` | |
149
- | `--transcript <acc>` | Specific transcript accession | MANE/RefSeq Select |
150
- | `--ref <rowname>` | Reference row = the transcript's CDS | first row |
151
- | `-o, --output <file>` | Output GFF file path | `genestructure.gff` |
213
+ #### Choosing a backend
152
214
 
153
215
  ```bash
154
- # F12 coding alignment -> 14-exon overlay (MANE Select transcript, human row)
155
- react-msaview-cli genestructure f12-cds.stock --gene F12 --ref human -o exons.gff
216
+ ## EBI web API — no install, but one sequential submission per sequence
217
+ react-msaview-cli interproscan alignment.fasta -o domains.gff --email you@example.com
156
218
 
157
- # pin a specific transcript
158
- react-msaview-cli genestructure aln.fa --transcript NM_000505.4 --ref human
159
- ```
160
-
161
- ### export-svg
219
+ ## Docker — no InterProScan install, whole alignment in one run
220
+ react-msaview-cli interproscan alignment.fasta -o domains.gff --docker
162
221
 
163
- Render an alignment (with an optional tree and domain overlay) straight to a
164
- standalone SVG — no browser required. This is what the R package shells out to
165
- for vector export.
222
+ ## a local install
223
+ react-msaview-cli interproscan alignment.fasta -o domains.gff \
224
+ --local --interproscan-path /opt/interproscan/interproscan.sh
166
225
 
167
- ```bash
168
- react-msaview-cli export-svg --msa <file> [options]
226
+ ## Singularity/Apptainer, for HPC clusters without Docker
227
+ react-msaview-cli interproscan alignment.fasta -o domains.gff \
228
+ --singularity --singularity-image /path/to/interproscan.sif
169
229
  ```
170
230
 
171
- #### Options
172
-
173
- | Option | Description | Default |
174
- | ------------------------ | --------------------------------------- | --------------- |
175
- | `--msa <file>` | MSA file (FASTA, Stockholm, or Clustal) | _required_ |
176
- | `--tree <file>` | Newick tree file | |
177
- | `--gff <file>` | InterProScan domain GFF file | |
178
- | `-o, --output <file>` | Output SVG file path | `alignment.svg` |
179
- | `--color-scheme <name>` | Color scheme | `maeditor` |
180
- | `--width <px>` | Canvas width in pixels | `1200` |
181
- | `--height <px>` | Canvas height in pixels | `600` |
182
- | `--tree-area-width <px>` | Tree panel width in pixels | |
231
+ Docker mounts a temp directory into the `interpro/interproscan` container, runs
232
+ the scan on the whole alignment at once, and reads the JSON back out.
183
233
 
184
- ```bash
185
- react-msaview-cli export-svg --msa alignment.fasta -o alignment.svg
186
- react-msaview-cli export-svg --msa alignment.fasta --tree tree.nwk -o alignment.svg
187
- react-msaview-cli export-svg --msa alignment.fasta --gff domains.gff \
188
- --color-scheme clustalx_protein_dynamic -o alignment.svg
189
- ```
234
+ The EBI API has usage limits: sequences go one at a time, sequentially, to avoid
235
+ overwhelming the server. Past about 100 sequences, use a local or container
236
+ backend.
190
237
 
191
- ## Examples
238
+ #### InterProScan programs
192
239
 
193
- ### Using the EBI API (recommended for small datasets)
240
+ `--programs` takes any combination of `PfamA` (in the default), `CDD` (in the
241
+ default), `SMART`, `SUPERFAMILY`, `Gene3D`, `PANTHER`, `TIGRFAM`, `Hamap`,
242
+ `ProSiteProfiles`, `ProSitePatterns`, `PRINTS`, `PIRSF`, and `MobiDBLite`.
194
243
 
195
244
  ```bash
196
- # Basic usage - runs the default PfamA + CDD analysis
197
- react-msaview-cli interproscan alignment.fasta -o domains.gff --email your@email.com
198
-
199
- # Multiple programs
200
245
  react-msaview-cli interproscan alignment.fasta -o domains.gff \
201
- --programs PfamA,SMART,Gene3D \
202
- --email your@email.com
246
+ --programs PfamA,SMART,Gene3D --email you@example.com
203
247
  ```
204
248
 
205
- ### Using local InterProScan
249
+ ### genestructure
206
250
 
207
- For large datasets or frequent usage, install InterProScan locally:
251
+ Build a **gene-structure GFF** for a coding-sequence alignment from a RefSeq
252
+ transcript, overlaid the same way InterProScan domains are. The exon model is
253
+ fetched from the NCBI Datasets v2 API; each species' Nth exon is named `exon-N`,
254
+ so a given exon is the same color in every row and the exon architecture reads
255
+ straight down the alignment.
208
256
 
209
257
  ```bash
210
- # With interproscan.sh in PATH
211
- react-msaview-cli interproscan alignment.fasta -o domains.gff --local
212
-
213
- # With custom path
214
- react-msaview-cli interproscan alignment.fasta -o domains.gff \
215
- --local \
216
- --interproscan-path /opt/interproscan/interproscan.sh
217
-
218
- # With specific programs
219
- react-msaview-cli interproscan alignment.fasta -o domains.gff \
220
- --local \
221
- --programs PfamA,SMART
258
+ react-msaview-cli genestructure <input-msa> --gene <symbol> --ref <rowname> [options]
222
259
  ```
223
260
 
224
- ### Using Docker
261
+ The exon boundaries of the chosen transcript are mapped onto the reference row's
262
+ columns, then projected into every other row's own ungapped coordinates — so an
263
+ exon that picks up a frameshifting indel in one lineage gets shorter on exactly
264
+ that row while staying column-aligned with the rest. The reference row must be
265
+ the transcript's coding sequence (the CLI warns if its length doesn't match).
225
266
 
226
- No local InterProScan install needed — just Docker:
267
+ | Option | Description | Default |
268
+ | --------------------- | --------------------------------------------- | ------------------- |
269
+ | `--gene <symbol>` | Gene symbol to look up in RefSeq (e.g. `F12`) | |
270
+ | `--taxon <name\|id>` | Taxon for `--gene` | `human` |
271
+ | `--gene-id <id>` | NCBI GeneID, instead of `--gene` | |
272
+ | `--transcript <acc>` | Specific transcript accession | MANE/RefSeq Select |
273
+ | `--ref <rowname>` | Reference row = the transcript's CDS | first row |
274
+ | `-o, --output <file>` | Output GFF file path | `genestructure.gff` |
227
275
 
228
276
  ```bash
229
- react-msaview-cli interproscan alignment.fasta -o domains.gff --docker
230
- ```
231
-
232
- This mounts a temp directory into the `interpro/interproscan` container, runs
233
- the scan on the whole alignment at once, and reads the JSON back out.
277
+ ## F12 coding alignment -> 14-exon overlay (MANE Select transcript, human row)
278
+ react-msaview-cli genestructure f12-cds.stock --gene F12 --ref human -o exons.gff
234
279
 
235
- ### Using Singularity / Apptainer
280
+ ## pin a specific transcript
281
+ react-msaview-cli genestructure aln.fa --transcript NM_000505.4 --ref human
282
+ ```
236
283
 
237
- On HPC clusters where Docker is unavailable:
284
+ ## Input formats
238
285
 
239
- ```bash
240
- # Pull from Docker Hub (requires network)
241
- react-msaview-cli interproscan alignment.fasta -o domains.gff --singularity
286
+ The CLI detects the MSA format from the file:
242
287
 
243
- # Or use a pre-pulled .sif image
244
- react-msaview-cli interproscan alignment.fasta -o domains.gff \
245
- --singularity \
246
- --singularity-image /path/to/interproscan.sif
247
- ```
248
-
249
- ### Different input formats
288
+ - **FASTA** (`.fasta`, `.fa`, `.faa`)
289
+ - **Clustal** (`.clustal`, `.aln`)
290
+ - **Stockholm** (`.sto`, `.stockholm`)
291
+ - **A3M** (`.a3m`) — AlphaFold/ColabFold
292
+ - **EMF** (`.emf`) — Ensembl Multi Format
250
293
 
251
- ```bash
252
- # Clustal format
253
- react-msaview-cli interproscan alignment.clustal -o domains.gff
294
+ ## Annotation output format
254
295
 
255
- # Stockholm format
256
- react-msaview-cli interproscan PF00001.stockholm -o domains.gff
296
+ The annotation commands write standard GFF3, one `protein_match` line per hit.
297
+ `start`/`end` are 1-based positions in the **ungapped** sequence (gaps are
298
+ stripped before scanning), and the attributes carry the signature accession,
299
+ name, and description:
257
300
 
258
- # A3M format (from ColabFold/AlphaFold)
259
- react-msaview-cli interproscan colabfold.a3m -o domains.gff
301
+ ```gff
302
+ ##gff-version 3
303
+ seq1 InterProScan protein_match 10 150 . . . Name=PF00001;signature_desc=7tm_1;description=7 transmembrane receptor (rhodopsin family)
304
+ seq1 InterProScan protein_match 200 350 . . . Name=PF00002;signature_desc=7tm_2;description=7 transmembrane receptor (Secretin family)
305
+ seq2 InterProScan protein_match 5 120 . . . Name=PF00001;signature_desc=7tm_1;description=7 transmembrane receptor (rhodopsin family)
260
306
  ```
261
307
 
262
- ## Worked example
308
+ A worked run:
263
309
 
264
310
  ```console
265
311
  $ react-msaview-cli interproscan gpcrs.fasta -o domains.gff --docker
@@ -274,85 +320,54 @@ Writing output to domains.gff...
274
320
  Done!
275
321
  ```
276
322
 
277
- ## Output format
323
+ ## Using the GFF elsewhere
278
324
 
279
- The output is standard GFF3, with one `protein_match` line per domain hit.
280
- `start`/`end` are 1-based positions in the **ungapped** sequence (gaps are
281
- stripped before scanning), and the attributes carry the signature accession,
282
- name, and description:
283
-
284
- ```gff
285
- ##gff-version 3
286
- seq1 InterProScan protein_match 10 150 . . . Name=PF00001;signature_desc=7tm_1;description=7 transmembrane receptor (rhodopsin family)
287
- seq1 InterProScan protein_match 200 350 . . . Name=PF00002;signature_desc=7tm_2;description=7 transmembrane receptor (Secretin family)
288
- seq2 InterProScan protein_match 5 120 . . . Name=PF00001;signature_desc=7tm_1;description=7 transmembrane receptor (rhodopsin family)
289
- ```
290
-
291
- ## Loading results in react-msaview
292
-
293
- After generating the GFF file, you can load it in react-msaview:
325
+ The same file the CLI writes loads into every other front end.
294
326
 
295
- - Open your MSA file in react-msaview
296
- - Select the generated GFF file in the import form's **Annotation GFF file or
297
- URL** field
298
- - Domains appear as colored boxes on the alignment
327
+ In the web viewer, select it in the import form's **Annotation GFF file or URL**
328
+ field. (The **Annotations > Open InterProScan results...** menu item takes
329
+ InterProScan JSON rather than GFF, so use the import form for the file generated
330
+ above.)
299
331
 
300
- The **Annotations > Open InterProScan results...** menu item takes InterProScan
301
- JSON rather than GFF, so use the import form for the file generated above.
302
-
303
- In the React component, pass it inline as the `gff` prop (see the "Protein
304
- domains" example in `packages/examples`):
332
+ In the React component, pass it inline as the `gff` prop:
305
333
 
306
334
  ```jsx
307
335
  <MSAViewer msa={msaText} gff={domainsGff} />
308
336
  ```
309
337
 
310
- From R, pass the file (or string) as the `gff` argument:
338
+ From R:
311
339
 
312
340
  ```r
313
341
  msaview(msa = "alignment.fasta", gff = "domains.gff")
314
342
  ```
315
343
 
316
- The domains render as labeled boxes over the matching rows:
317
-
318
- ![InterProScan domains rendered over an alignment](../../docs/media/example-domains.svg)
319
-
320
344
  ## Troubleshooting
321
345
 
322
- ### EBI API timeout
323
-
324
- If you get timeout errors with the EBI API:
325
-
326
- - Use `--local`, `--docker`, or `--singularity` to run InterProScan yourself
327
- - Check your internet connection
328
- - For large datasets, a local/container backend is much faster than the API
346
+ **EBI API timeout.** Use `--local`, `--docker`, or `--singularity` to run
347
+ InterProScan yourself. For large datasets those are much faster than the API
348
+ regardless.
329
349
 
330
- ### Local InterProScan not found
350
+ **Local InterProScan not found.**
331
351
 
332
352
  ```
333
353
  Error: Failed to run Local: spawn interproscan.sh ENOENT. Is interproscan.sh installed and on PATH?
334
354
  ```
335
355
 
336
- Make sure InterProScan is installed and specify the full path:
356
+ Give the full path:
357
+ `--interproscan-path /full/path/to/interproscan-5.xx/interproscan.sh`
337
358
 
338
- ```bash
339
- --interproscan-path /full/path/to/interproscan-5.xx/interproscan.sh
340
- ```
341
-
342
- ### No results in output
359
+ **No results in the output.** Check that the sequences are protein, not
360
+ nucleotide; try other `--programs`; verify the input parses as one of the
361
+ formats above.
343
362
 
344
- - Check that your sequences are protein sequences (not nucleotide)
345
- - Try different programs (some may not have hits for your sequences)
346
- - Verify the input file is valid MSA format
363
+ **The exported figure is enormous.** `export-svg` draws the whole alignment at
364
+ `--col-width` per column. Drop `--col-width` until it fits — below ~8px the
365
+ residue letters stop drawing, which is most of the file size.
347
366
 
348
- ## API rate limits
367
+ ## Uses
349
368
 
350
- The EBI InterProScan API has usage limits:
351
-
352
- - Sequences are submitted one at a time, sequentially, to avoid overwhelming the
353
- server
354
- - For large datasets (>100 sequences), use `--local`, `--docker`, or
355
- `--singularity` instead
369
+ [msa-parsers](https://github.com/GMOD/JBrowseMSA/tree/main/packages/msa-parsers)
370
+ for file format support, and [react-msaview](../lib) for rendering.
356
371
 
357
372
  ## License
358
373
 
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "react-msaview-cli",
3
- "version": "6.1.1",
3
+ "version": "6.2.1",
4
4
  "license": "MIT",
5
5
  "type": "module",
6
6
  "repository": {
@@ -28,8 +28,8 @@
28
28
  "mobx-react": "^10.0.0",
29
29
  "react": "^19.2.8",
30
30
  "react-dom": "^19.2.8",
31
- "msa-parsers": "6.1.1",
32
- "react-msaview": "6.1.1"
31
+ "msa-parsers": "6.2.1",
32
+ "react-msaview": "6.2.1"
33
33
  },
34
34
  "scripts": {
35
35
  "clean": "node --eval \"fs.rmSync('dist',{recursive:true,force:true})\" --input-type=module",