@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

# From the monorepo root
yarn install
yarn workspace @react-msaview/cli build

# Or install globally (after publishing)
npm install -g @react-msaview/cli

Commands

interproscan

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

react-msaview-cli interproscan <input-msa> [options]

Options

| Option | Description | Default | | ---------------------------- | ------------------------------------------------------ | ------------------ | | -o, --output <file> | Output GFF file path | domains.gff | | --local | Use local InterProScan installation instead of EBI API | false | | --interproscan-path <path> | Path to local interproscan.sh | interproscan.sh | | --programs <list> | Comma-separated list of InterProScan programs | Pfam | | --email <email> | Email for EBI API (required for EBI API usage) | [email protected] | | --batch-size <n> | 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

Using EBI API (recommended for small datasets)

# Basic usage - runs Pfam analysis
react-msaview-cli interproscan alignment.fasta -o domains.gff --email [email protected]

# Multiple programs
react-msaview-cli interproscan alignment.fasta -o domains.gff \
  --programs Pfam,SMART,Gene3D \
  --email [email protected]

# Smaller batch size for large sequences
react-msaview-cli interproscan large_proteins.fasta -o domains.gff \
  --batch-size 10 \
  --email [email protected]

Using Local InterProScan

For large datasets or frequent usage, install InterProScan locally:

# 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

Different Input Formats

# 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-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

EBI API Timeout

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

Local InterProScan Not Found

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

Make sure InterProScan is installed and specify the full path:

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

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

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