@react-msaview/cli

Command-line tools for react-msaview (JBrowseMSA), including batch
InterProScan processing for multiple sequence alignments.

Uses msa-parsers for file format support.

Installation

``bash


From the monorepo root

yarn install
yarn workspace @react-msaview/cli build

Or install globally (after publishing)

npm install -g @react-msaview/cli
`

Commands

$3

Run InterProScan on all sequences in an MSA file and output results as GFF3.

`bash
react-msaview-cli interproscan [options]
`

#### Options

| Option | Description | Default |
| ---------------------------- | ------------------------------------------------------ | ------------------ |
| -o, --output | Output GFF file path | domains.gff |
| --local | Use local InterProScan installation instead of EBI API | false |
| --interproscan-path | Path to local interproscan.sh | interproscan.sh |
| --programs | Comma-separated list of InterProScan programs | Pfam |
| --email | Email for EBI API (required for EBI API usage) | user@example.com |
| --batch-size | Number of sequences per API batch | 30 |
| -h, --help | Show help message | |

#### Supported MSA Formats

The CLI automatically detects the input format:

- FASTA (.fasta, .fa, .faa)
- Clustal (.clustal, .aln)
- Stockholm (.sto, .stockholm)
- A3M (.a3m) - AlphaFold/ColabFold format
- EMF (.emf) - Ensembl Multi Format

#### Available InterProScan Programs

When using --programs, you can specify any combination of:

- Pfam - Protein families (default)
- SMART - Simple Modular Architecture Research Tool
- SUPERFAMILY - Structural and functional annotation
- Gene3D - Structural domain assignments
- CDD - Conserved Domain Database
- PANTHER - Protein Analysis Through Evolutionary Relationships
- TIGRFAM - TIGR protein families
- Hamap - High-quality Automated Annotation of Microbial Proteomes
- ProSiteProfiles - PROSITE profiles
- ProSitePatterns - PROSITE patterns
- PRINTS - Protein fingerprints
- PIRSF - PIR SuperFamily
- MobiDBLite - Disorder prediction

Examples

$3

`bash


Basic usage - runs Pfam 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 \
--email your@email.com

Smaller batch size for large sequences

react-msaview-cli interproscan large_proteins.fasta -o domains.gff \
--batch-size 10 \
--email your@email.com
`

$3

For large datasets or frequent usage, install InterProScan locally:

`bash


With interproscan.sh in PATH

react-msaview-cli interproscan alignment.fasta -o domains.gff --local

With custom path

react-msaview-cli interproscan alignment.fasta -o domains.gff \
--local \
--interproscan-path /opt/interproscan/interproscan.sh

With specific programs

react-msaview-cli interproscan alignment.fasta -o domains.gff \
--local \
--programs Pfam,SMART
`

$3

`bash


Clustal format

react-msaview-cli interproscan alignment.clustal -o domains.gff

Stockholm format

react-msaview-cli interproscan PF00001.stockholm -o domains.gff

A3M format (from ColabFold/AlphaFold)

react-msaview-cli interproscan colabfold.a3m -o domains.gff
`

Output Format

The output is standard GFF3 format compatible with react-msaview:

`gff
##gff-version 3
seq1 InterProScan protein_match 10 150 . . . Name=PF00001;signature_desc=7tm_1;description=7 transmembrane receptor (rhodopsin family)
seq1 InterProScan protein_match 200 350 . . . Name=PF00002;signature_desc=7tm_2;description=7 transmembrane receptor (Secretin family)
seq2 InterProScan protein_match 5 120 . . . Name=PF00001;signature_desc=7tm_1;description=7 transmembrane receptor (rhodopsin family)
`

Loading Results in react-msaview

After generating the GFF file, you can load it in react-msaview:

1. Open your MSA file in react-msaview
2. Go to Menu > Open domains...
3. Select the generated GFF file
4. Domains will appear as colored boxes on the alignment

Troubleshooting

$3

If you get timeout errors with the EBI API:

- Reduce --batch-size (try 10-20 for large proteins)
- Use --local with a local InterProScan installation
- Check your internet connection

$3

`
Error: Failed to run InterProScan: spawn interproscan.sh ENOENT
`

Make sure InterProScan is installed and specify the full path:

`bash
--interproscan-path /full/path/to/interproscan-5.xx/interproscan.sh
`

$3

- 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

The EBI InterProScan API has usage limits:

- Maximum ~30 sequences per request (configurable via --batch-size`)
- Requests are processed sequentially to avoid overwhelming the server
- For large datasets (>100 sequences), consider using local InterProScan

License

MIT