interpro-manager

interpro-manager

CLI tool for interacting with EMBL-EBI's InterPro protein database — download protein records by taxonomy and submit sequences to InterProScan6 for analysis.

Contents

• Prerequisites
• Install
• Commands
  • download
  • scan
• Project Structure
  • Packages
• Development

Prerequisites

• Go 1.25+
• A valid email address (required for scan — any email works)

Install

go install github.com/dictybase/interpro-manager/cmd/interpro-cli@latest

Or build from source:

git clone https://github.com/dictybase/interpro-manager.git
cd interpro-manager
go build -o interpro-manager ./cmd/interpro-cli

Commands

download

Fetch InterPro protein records for a taxonomy ID, filter results that contain a gene symbol, and save as TSV.

interpro-manager download [--taxon-id ID] [--output FILE] [--page-size N]

Example:

# Download D. discoideum proteins (default)
interpro-manager download

# Download proteins for a different organism with custom output
interpro-manager download --taxon-id 9606 --output human_proteins.tsv --page-size 50

The TSV output contains the following columns:

scan

Submit protein sequences from FASTA files to the InterProScan6 job dispatcher, poll for completion, and download JSON results.

interpro-manager scan --fasta FILE --email ADDRESS [--output DIR] [--seq-type TYPE] [--poll-interval DURATION] [--timeout DURATION]

Example:

# Set email and scan a FASTA file
export EBI_EMAIL=yourname@example.com
interpro-manager scan --fasta proteins.fa

# Custom output directory with shorter polling
interpro-manager scan \
  --fasta proteins.fa \
  --email yourname@example.com \
  --output results/ \
  --poll-interval 5s \
  --timeout 300s

Results are saved as {sequence-id}_{job-id}.json in the output directory, one file per FASTA record.

Project Structure

.
├── cmd/
│   └── interpro-cli/
│       └── main.go              # CLI entry point, command registration
├── internal/
│   ├── interpro/
│   │   ├── command.go           # download subcommand
│   │   ├── client.go            # HTTP client, JSON deserialization
│   │   ├── extract.go           # TSV formatting, gene filter
│   │   ├── loop.go              # Pagination loop for download
│   │   ├── model.go             # API response types
│   │   ├── scan.go              # scan subcommand orchestrator
│   │   ├── scan_loop.go         # FASTA record streaming
│   │   ├── scan_model.go        # Scan request/job types
│   │   ├── scan_poll.go         # Job status polling
│   │   ├── scan_result.go       # Result download
│   │   ├── scan_submit.go       # Job submission
│   │   └── tsv.go               # File I/O utilities
│   └── seqio/
│       ├── fasta.go             # FASTA parser
│       └── fasta_test.go        # FASTA parser tests
└── docs/
    └── ...                      # Design docs and reference material

Packages

Both packages are built with fp-go functional programming combinators and use urfave/cli for the CLI framework.

Development

# Run tests
gotestsum --format pkgname-and-test-fails --format-hide-empty-pkg -- ./...

# Run tests with verbose output
gotestsum --format testdox --format-hide-empty-pkg -- ./...

# Lint
golangci-lint run ./...

# Format
golangci-lint fmt

# Build
go build -o interpro-manager ./cmd/interpro-cli

Sources

• InterPro API documentation
• InterProScan6 API