Ena Sequence API

# Search for studies
curl "https://www.ebi.ac.uk/ena/portal/api/search?query=CRISPR+cas9&result=study&limit=20&format=json"

# Search for samples
curl "https://www.ebi.ac.uk/ena/portal/api/search?query=human+gut+microbiome&result=sample&limit=20&format=json"

# Search for runs (sequencing data)
curl "https://www.ebi.ac.uk/ena/portal/api/search?query=RNA-seq+cancer&result=read_run&limit=20&format=json"

# Get record by accession
curl "https://www.ebi.ac.uk/ena/browser/api/xml/PRJEB12345"

# Get in JSON format
curl "https://www.ebi.ac.uk/ena/browser/api/summary/PRJEB12345"

# Get sequence in FASTA
curl "https://www.ebi.ac.uk/ena/browser/api/fasta/AF123456"

# Get in EMBL flat file format
curl "https://www.ebi.ac.uk/ena/browser/api/embl/AF123456"

# Search by organism
curl "https://www.ebi.ac.uk/ena/portal/api/search?query=tax_tree(9606)&result=study&limit=20&format=json"

# Get taxonomy details
curl "https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/9606"

import requests

PORTAL_URL = "https://www.ebi.ac.uk/ena/portal/api"
BROWSER_URL = "https://www.ebi.ac.uk/ena/browser/api"


def search_studies(query: str, limit: int = 20) -> list:
    """Search ENA for research studies."""
    params = {
        "query": query,
        "result": "study",
        "limit": limit,
        "format": "json",
        "fields": "study_accession,study_title,study_description,"
                  "tax_id,scientific_name,center_name",
    }
    resp = requests.get(f"{PORTAL_URL}/search", params=params)
    resp.raise_for_status()
    return resp.json()


def search_runs(query: str, limit: int = 20) -> list:
    """Search for sequencing runs."""
    params = {
        "query": query,
        "result": "read_run",
        "limit": limit,
        "format": "json",
        "fields": "run_accession,experiment_title,instrument_platform,"
                  "library_strategy,read_count,base_count",
    }
    resp = requests.get(f"{PORTAL_URL}/search", params=params)
    resp.raise_for_status()
    return resp.json()


def get_fasta(accession: str) -> str:
    """Retrieve sequence in FASTA format."""
    resp = requests.get(f"{BROWSER_URL}/fasta/{accession}")
    resp.raise_for_status()
    return resp.text


def get_study_runs(study_accession: str) -> list:
    """Get all sequencing runs for a study."""
    params = {
        "query": f'study_accession="{study_accession}"',
        "result": "read_run",
        "format": "json",
        "fields": "run_accession,fastq_ftp,read_count,base_count",
        "limit": 1000,
    }
    resp = requests.get(f"{PORTAL_URL}/search", params=params)
    resp.raise_for_status()
    return resp.json()


# Example: find COVID-19 sequencing studies
studies = search_studies("SARS-CoV-2 whole genome", limit=5)
for s in studies:
    print(f"{s['study_accession']}: {s['study_title']}")
    print(f"  Organism: {s.get('scientific_name')}")

# Example: find RNA-seq runs
runs = search_runs("RNA-seq breast cancer", limit=5)
for r in runs:
    reads = int(r.get("read_count", 0))
    print(f"{r['run_accession']}: {r.get('experiment_title', '')}")
    print(f"  Platform: {r.get('instrument_platform')} | "
          f"Reads: {reads:,}")

# Download FASTQ files (from run metadata)
# The fastq_ftp field provides FTP paths:
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR123/ERR123456/ERR123456_1.fastq.gz

# Bulk download via Aspera (faster)
ascp -QT -l 300m -P33001 \
  era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/ERR123/ERR123456/ ./