Reference Sequence Management

Reference Sequence Management

The refget module handles reference sequence retrieval and digest computation, following the refget protocol for sequence identification.

RefgetStore

RefgetStore manages reference sequences and their digests:

import gtars

# Create RefgetStore
store = gtars.RefgetStore()

# Add sequence
store.add_sequence("chr1", sequence_data)

# Retrieve sequence
seq = store.get_sequence("chr1")

# Get sequence digest
digest = store.get_digest("chr1")

Sequence Digests

Compute and verify sequence digests:

# Compute digest for sequence
from gtars.refget import compute_digest

digest = compute_digest(sequence_data)

# Verify digest matches
is_valid = store.verify_digest("chr1", expected_digest)

Integration with Reference Genomes

Work with standard reference genomes:

# Load reference genome
store = gtars.RefgetStore.from_fasta("hg38.fa")

# Get chromosome sequences
chr1 = store.get_sequence("chr1")
chr2 = store.get_sequence("chr2")

# Get subsequence
region_seq = store.get_subsequence("chr1", 1000, 2000)

CLI Usage

Manage reference sequences from command line:

# Compute digest for FASTA file
gtars refget digest --input genome.fa --output digests.txt

# Verify sequence digest
gtars refget verify --sequence sequence.fa --digest expected_digest

Refget Protocol Compliance

The refget module follows the GA4GH refget protocol:

Digest Computation

Digests are computed using SHA-512 truncated to 48 bytes:

# Compute refget-compliant digest
digest = gtars.refget.compute_digest(sequence)
# Returns: "SQ.abc123..."

Sequence Retrieval

Retrieve sequences by digest:

# Get sequence by refget digest
seq = store.get_sequence_by_digest("SQ.abc123...")

Use Cases

Reference Validation

Verify reference genome integrity:

# Compute digests for reference
store = gtars.RefgetStore.from_fasta("reference.fa")
digests = {chrom: store.get_digest(chrom) for chrom in store.chromosomes}

# Compare with expected digests
for chrom, expected in expected_digests.items():
    actual = digests[chrom]
    if actual != expected:
        print(f"Mismatch for {chrom}: {actual} != {expected}")

Sequence Extraction

Extract specific genomic regions:

# Extract regions of interest
store = gtars.RefgetStore.from_fasta("hg38.fa")

regions = [
    ("chr1", 1000, 2000),
    ("chr2", 5000, 6000),
    ("chr3", 10000, 11000)
]

sequences = [store.get_subsequence(c, s, e) for c, s, e in regions]

Cross-Reference Comparison

Compare sequences across different references:

# Load two reference versions
hg19 = gtars.RefgetStore.from_fasta("hg19.fa")
hg38 = gtars.RefgetStore.from_fasta("hg38.fa")

# Compare digests
for chrom in hg19.chromosomes:
    digest_19 = hg19.get_digest(chrom)
    digest_38 = hg38.get_digest(chrom)
    if digest_19 != digest_38:
        print(f"{chrom} differs between hg19 and hg38")

Performance Notes

• Sequences loaded on demand
• Digests cached after computation
• Efficient subsequence extraction
• Memory-mapped file support for large genomes