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Refget CLI Reference

The refget command-line interface provides tools for working with reference sequences following GA4GH standards. It includes commands for computing sequence collection digests, managing local sequence stores, and interacting with remote seqcol APIs.

Installation

pip install refget

Quick Start

# Compute seqcol digest from a FASTA file
refget fasta digest genome.fa

# Create all index files from a FASTA
refget fasta index genome.fa

# Initialize a local sequence store
refget store init

# Add a FASTA to the store
refget store add genome.fa

# Compare two sequence collections
refget seqcol compare genome1.fa genome2.fa

Command Groups

The CLI is organized into five command groups:

Group Description
refget config Configuration management
refget fasta FASTA file utilities
refget store RefgetStore operations
refget seqcol Sequence collection API
refget admin Admin/database operations

Global Options

--version, -v    Show version and exit
--help           Show help message and exit

Config Commands

Manage refget configuration stored in ~/.refget/config.toml.

config init

Interactive setup wizard for refget configuration.

refget config init [--force]

Options:

  • --force, -f: Overwrite existing configuration

config show

View all configuration or a specific section.

refget config show [SECTION]

Arguments:

  • SECTION: Optional section to show (store, seqcol_servers, remote_stores, admin)

config get

Get a specific configuration value.

refget config get KEY

Examples: 

refget config get store.path
refget config get admin.postgres_host

config set

Set a configuration value.

refget config set KEY VALUE

Examples: 

refget config set store.path /path/to/store
refget config set admin.postgres_host localhost

config path

Show the path to the configuration file.

refget config path

config validate

Validate the configuration file.

refget config validate

config add

Add a server or store to the configuration.

refget config add RESOURCE_TYPE URL [--name NAME]

Arguments:

  • RESOURCE_TYPE: One of: seqcol_server, remote_store, or sequence_server
  • URL: URL of the server/store to add

Options:

  • --name, -n: Optional name for this server/store

Examples: 

refget config add seqcol_server https://seqcolapi.databio.org --name databio
refget config add remote_store s3://bucket/store/ --name primary
refget config add sequence_server https://www.ebi.ac.uk/ena/cram/ --name ebi

config remove

Remove a server or store from the configuration.

refget config remove RESOURCE_TYPE NAME

Examples: 

refget config remove seqcol_server databio
refget config remove remote_store primary

FASTA Commands

Utilities for processing FASTA files and computing seqcol data.

fasta digest

Compute the seqcol digest (top-level) of a FASTA file.

refget fasta digest FILE

Output: JSON with digest and file path 

{"digest": "abc123...", "file": "genome.fa"}

fasta seqcol

Compute the full seqcol JSON from a FASTA file.

refget fasta seqcol FILE [-o OUTPUT] [-l LEVEL]

Options:

  • --output, -o: Output file path (default: stdout)
  • --level, -l: Seqcol level: 1 (digests only) or 2 (full arrays). Default: 2

Example: 

refget fasta seqcol genome.fa -o genome.seqcol.json

fasta index

Generate ALL derived files from a FASTA file.

refget fasta index FILE [-o OUTPUT_DIR] [--json]

For genome.fa, creates:

  • genome.fa.fai - FASTA index (samtools-compatible)
  • genome.seqcol.json - Sequence collection JSON
  • genome.chrom.sizes - Chromosome sizes

Options:

  • --output-dir, -o: Output directory (default: same as input file)
  • --json, -j: Output result as JSON

fasta fai

Compute FAI index from a FASTA file.

refget fasta fai FILE [-o OUTPUT]

Outputs samtools-compatible .fai format (tab-separated).

fasta chrom-sizes

Compute chrom.sizes from a FASTA file.

refget fasta chrom-sizes FILE [-o OUTPUT]

Outputs UCSC-compatible chrom.sizes format (tab-separated name/length).

fasta stats

Display statistics for a FASTA file.

refget fasta stats FILE [--json]

Shows: sequence count, total length, N50, min/max/mean sequence length.

Options:

  • --json, -j: Output as JSON instead of table

fasta validate

Validate a FASTA file format.

refget fasta validate FILE

Returns exit code 0 if valid, non-zero if invalid.

fasta rgsi

Compute .rgsi (RefgetStore sequence index) from a FASTA file.

refget fasta rgsi FILE [-o OUTPUT]

The .rgsi file contains sequence metadata in RefgetStore format.

fasta rgci

Compute .rgci (RefgetStore collection index) from a FASTA file.

refget fasta rgci FILE [-o OUTPUT]

The .rgci file contains collection metadata in RefgetStore format.

Store Commands

Manage a local RefgetStore for storing and retrieving sequences.

store init

Initialize a local RefgetStore.

refget store init [--path PATH]

Options:

  • --path, -p: Path for the store (default: from config or ~/.refget/store)

store add

Import a FASTA file to the local store.

refget store add FASTA [--path PATH] [--mode MODE]

Options:

  • --path, -p: Store path (default: from config)
  • --mode, -m: Storage mode: encoded (compressed, ~4x smaller, default) or raw (faster access)

Output: JSON with digest and sequence count 

{"digest": "abc123...", "fasta": "/path/to/file.fa", "sequences": 25}

Examples: 

# Add with default encoding (compressed)
refget store add genome.fa

# Add with raw encoding (faster access)
refget store add genome.fa --mode raw

store list

List collections in the store.

refget store list [--path PATH] [--server URL]

Options:

  • --path, -p: Store path (default: from config)
  • --server, -s: Remote store URL (overrides --path)

Output: 

{"collections": [{"digest": "abc123..."}, {"digest": "def456..."}]}

store get

Get a collection by digest.

refget store get DIGEST [--path PATH] [--server URL]

Options:

  • --path, -p: Store path (default: from config)
  • --server, -s: Remote store URL (overrides --path)

Output: Full seqcol with names, lengths, and sequences arrays.

store pull

Pull a collection from a remote store to local store.

refget store pull DIGEST [--server URL] [--path PATH]

Options:

  • --server, -s: Remote store URL to pull from
  • --path, -p: Local store path (default: from config)

store export

Export a collection as a FASTA file.

refget store export DIGEST [-o OUTPUT] [--bed BED] [--name NAME] [--path PATH]

Options:

  • --output, -o: Output FASTA file path (default: stdout)
  • --bed, -b: BED file for region extraction
  • --name, -n: Sequence names to include (can be repeated)
  • --line-width, -w: FASTA line width (default: 80)

Examples: 

# Export full collection
refget store export abc123 -o genome.fa

# Export specific chromosomes
refget store export abc123 -o subset.fa --name chr1 --name chr2

# Export regions from BED file
refget store export abc123 -o regions.fa --bed regions.bed

store seq

Get a sequence or subsequence.

refget store seq DIGEST [--name NAME] [--start N] [--end M] [--path PATH]

Examples: 

# Full sequence by digest
refget store seq <seq_digest>

# Subsequence
refget store seq <seq_digest> --start 100 --end 200

# By collection and name
refget store seq <coll_digest> --name chr1

# Subsequence by name
refget store seq <coll_digest> --name chr1 --start 100 --end 200

store fai

Generate .fai index from a collection digest.

refget store fai DIGEST [-o OUTPUT] [--path PATH]

store chrom-sizes

Generate chrom.sizes from a collection digest.

refget store chrom-sizes DIGEST [-o OUTPUT] [--path PATH]

store stats

Display store statistics.

refget store stats [--path PATH]

Output: 

{"collections": 3, "sequences": 75, "storage_mode": "Encoded"}

store remove

Remove a collection from the store.

refget store remove DIGEST [--path PATH]

Seqcol Commands

Work with sequence collections and the seqcol API.

seqcol compare

Compare two sequence collections.

refget seqcol compare A B [--server URL] [--quiet]

Accepts flexible inputs:

  • <digest> - Fetches from local store or server
  • <file.fa> - Computes seqcol on the fly
  • <file.seqcol.json> - Uses local seqcol file

Options:

  • --server, -s: Server URL override
  • --quiet, -q: Suppress output; use exit code only (0=compatible, 1=incompatible)

Example: 

refget seqcol compare genome1.fa genome2.fa
refget seqcol compare abc123 def456 --server https://seqcolapi.databio.org

seqcol digest

Compute the seqcol digest of a file.

refget seqcol digest FILE

Accepts either a FASTA file or a .seqcol.json file.

seqcol validate

Validate a seqcol JSON file.

refget seqcol validate FILE

Checks that the file is valid JSON and conforms to the seqcol schema.

seqcol attributes

List attributes in a seqcol JSON file.

refget seqcol attributes FILE

Shows the attribute names and their array lengths.

seqcol schema

Show the seqcol schema definition.

refget seqcol schema

seqcol servers

List known seqcol servers from configuration.

refget seqcol servers

seqcol show

Get a sequence collection by digest from local store or remote server.

refget seqcol show DIGEST [--level LEVEL] [--server URL]

Resolution order: local store -> configured seqcol_servers -> --server override

Options:

  • --level, -l: Seqcol level: 1 (digests only) or 2 (full arrays). Default: 2
  • --server, -s: Server URL override

Examples: 

refget seqcol show XZlrcEGi6mlopZ2uD8ObHkQB1d0oDwKk
refget seqcol show XZlrcEGi6mlopZ2uD8ObHkQB1d0oDwKk --level 1
refget seqcol show XZlrcEGi6mlopZ2uD8ObHkQB1d0oDwKk --server https://seqcolapi.databio.org

seqcol list

List collections available on the server.

refget seqcol list [--server URL] [--limit N] [--offset N]

Options:

  • --server, -s: Server URL override
  • --limit, -n: Maximum number of collections to return (default: 100)
  • --offset: Offset for pagination (default: 0)

Find collections that share an attribute.

refget seqcol search [--names DIGEST] [--lengths DIGEST] [--sequences DIGEST] [--server URL]

The attribute digest is the digest of an attribute array (e.g., from level 1 output).

Options:

  • --names: Names array digest to search for
  • --lengths: Lengths array digest to search for
  • --sequences: Sequences array digest to search for
  • --server, -s: Server URL override

Example workflow: 

# Get names digest from level 1
names_digest=$(refget fasta seqcol genome.fa --level 1 | jq -r '.names')

# Search for collections with same names
refget seqcol search --names $names_digest

seqcol attribute

Retrieve the actual array values for an attribute digest.

refget seqcol attribute ATTRIBUTE_NAME DIGEST [--server URL]

Examples: 

refget seqcol attribute lengths cGRMZIb3AVgkcAfNv39RN7hnT5Chk7RX
refget seqcol attribute names Fw1r9eRxfOZD98KKrhlYQNEdSRHoVxAG

seqcol info

Get server information and capabilities.

refget seqcol info [--server URL]

Returns service info including supported algorithms and features.

Admin Commands

Database administration and bulk loading operations.

admin status

Show admin/database connection status.

refget admin status

Tests the database connection and displays connection info and table statistics.

admin info

Show system info (version, dependencies, etc.).

refget admin info [--json]

admin load

Load seqcol metadata from FASTA or JSON into PostgreSQL.

refget admin load [INPUT_FILE] [--pep PEP] [--pephub PROJECT] [--fa-root PATH] [--name NAME]

Can load from:

  • Single FASTA file
  • Single .seqcol.json file
  • Batch from PEP project file (--pep)
  • Batch from PEPhub project (--pephub)

Options:

  • --pep: PEP project file for batch loading
  • --pephub: PEPhub project (e.g., nsheff/human_fasta_ref)
  • --fa-root: Root directory for FASTA files (used with --pep/--pephub)
  • --name, -n: Human-readable name for the FASTA

Examples: 

refget admin load genome.fa
refget admin load genome.fa --name "Human GRCh38"
refget admin load genome.seqcol.json
refget admin load --pep genomes.yaml --fa-root /data/fasta
refget admin load --pephub nsheff/human_fasta_ref --fa-root /data/fasta

admin register

Upload a FASTA file to S3 and create a DRS record.

refget admin register FASTA --bucket BUCKET [--prefix PREFIX] [--cloud CLOUD] [--region REGION] [--digest DIGEST]

Does NOT load seqcol metadata. Use ingest for combined operation, or run load first.

Required Options:

  • --bucket, -b: S3 bucket name for upload

Optional Options:

  • --prefix, -p: S3 key prefix (default: none)
  • --cloud, -c: Cloud provider (default: aws)
  • --region, -r: Cloud region (default: us-east-1)
  • --digest, -d: Seqcol digest (if not provided, will be computed from FASTA)

Examples: 

refget admin register genome.fa --bucket my-refget-bucket
refget admin register genome.fa -b my-bucket -p fasta/ -c aws -r us-west-2
refget admin register genome.fa -b my-bucket --digest abc123...

admin ingest

Load seqcol metadata AND register FASTA with cloud storage (combined operation).

refget admin ingest [FASTA] --bucket BUCKET [--prefix PREFIX] [--cloud CLOUD] [--region REGION] [--pep PEP] [--pephub PROJECT] [--fa-root PATH] [--name NAME]

Combines load and register in a single operation:

  1. Parse FASTA and extract seqcol metadata
  2. Store metadata in PostgreSQL
  3. Upload FASTA to S3
  4. Create DRS record for access

Required Options:

  • --bucket, -b: S3 bucket name for upload

Optional Options:

  • --prefix, -p: S3 key prefix
  • --cloud, -c: Cloud provider (default: aws)
  • --region, -r: Cloud region (default: us-east-1)
  • --pep: PEP project file for batch ingestion
  • --pephub: PEPhub project (e.g., nsheff/human_fasta_ref)
  • --fa-root: Root directory for FASTA files (used with --pep/--pephub)
  • --name, -n: Human-readable name for the FASTA

Examples: 

refget admin ingest genome.fa --bucket my-bucket
refget admin ingest genome.fa -b my-bucket --name "Human GRCh38"
refget admin ingest --pep genomes.yaml --fa-root /data/fasta --bucket my-bucket

Environment Variables

Variable Description
REFGET_CONFIG Path to configuration file
REFGET_STORE Path to local RefgetStore
REFGET_STORE_PATH Alternative for store path
REFGET_DATABASE_URL PostgreSQL connection URL
POSTGRES_HOST Database host
POSTGRES_DB Database name
POSTGRES_USER Database user
POSTGRES_PASSWORD Database password

Exit Codes

Code Meaning
0 Success
1 General failure
2 File not found
3 Network error
4 Configuration error

Configuration File

The configuration file is located at ~/.refget/config.toml:

[store]
path = "~/.refget/store"

[seqcol_servers]
default = "https://seqcolapi.databio.org"

[admin]
postgres_host = "localhost"
postgres_db = "refget"
postgres_user = "postgres"