Tooluniverse Sequence Retrieval

# Sequence Retrieval Checklist

Use this checklist to ensure complete sequence profiles.

## Disambiguation

- [ ] Organism confirmed (scientific name)
- [ ] Gene symbol/name identified
- [ ] Sequence type determined (genomic/mRNA/protein)
- [ ] Strain specified (if relevant)
- [ ] Accession prefix identified → tool selection

## Accession Type Handling

- [ ] RefSeq (NC_, NM_, NP_, XM_) → NCBI tools only
- [ ] GenBank (U*, M*, CP*, etc.) → NCBI or ENA
- [ ] ENA tools NOT used with RefSeq accessions

## Per Sequence (Required)

- [ ] Accession number
- [ ] Organism (scientific name)
- [ ] Sequence type (DNA/RNA/protein)
- [ ] Length
- [ ] Curation level (●●●●/●●●○/●●○○/●○○○/○○○○)
- [ ] Database source

## Sequence Details

- [ ] Definition/title
- [ ] Molecule type (DNA/mRNA/protein)
- [ ] Topology (linear/circular)
- [ ] Sequence preview (first 100-200 bp)

## Annotations (If GenBank Format)

- [ ] CDS count and examples
- [ ] Gene count
- [ ] Other features noted

## Cross-References

- [ ] RefSeq accession (if exists)
- [ ] GenBank accession
- [ ] ENA compatibility noted
- [ ] BioProject/BioSample links

## Download Options

- [ ] FASTA format command shown
- [ ] GenBank format command shown
- [ ] Direct database links provided

## Report Quality

- [ ] Search process NOT shown in output
- [ ] Curation level tiers applied
- [ ] Alternative sequences listed
- [ ] Retrieval date included

## Error Handling

- [ ] No results → broader search suggested
- [ ] ENA 404 → recognized as RefSeq, NCBI used
- [ ] Large sequences → download link instead of preview


# Sequence Retrieval Examples

## Example 1: Find E. coli K-12 Genome

```python
from tooluniverse import ToolUniverse
tu = ToolUniverse()
tu.load_tools()

# Search
result = tu.tools.NCBI_search_nucleotide(
    operation="search",
    organism="Escherichia coli",
    strain="K-12",
    seq_type="complete_genome",
    limit=3
)

# Get accessions
accessions = tu.tools.NCBI_fetch_accessions(
    operation="fetch_accession",
    uids=result["data"]["uids"]
)

# Get sequence (RefSeq reference)
sequence = tu.tools.NCBI_get_sequence(
    operation="fetch_sequence",
    accession="NC_000913.3",
    format="fasta"
)

print(f"Genome size: {len(sequence['data'])} characters")
```

## Example 2: Get Human BRCA1 Gene

```python
# Search for BRCA1
result = tu.tools.NCBI_search_nucleotide(
    operation="search",
    organism="Homo sapiens",
    gene="BRCA1",
    limit=5
)

print(f"Found {result['data']['count']} BRCA1 sequences")

# Get top accessions
accessions = tu.tools.NCBI_fetch_accessions(
    operation="fetch_accession",
    uids=result["data"]["uids"]
)

# Get mRNA sequence with annotations
genbank = tu.tools.NCBI_get_sequence(
    operation="fetch_sequence",
    accession=accessions["data"][0],
    format="genbank"
)
```

## Example 3: SARS-CoV-2 Reference Genome

```python
# Search for reference genome
result = tu.tools.NCBI_search_nucleotide(
    operation="search",
    organism="SARS-CoV-2",
    keywords="reference genome Wuhan",
    limit=1
)

# Get accession (NC_045512)
accessions = tu.tools.NCBI_fetch_accessions(
    operation="fetch_accession",
    uids=result["data"]["uids"]
)

# Download complete genome
genome = tu.tools.NCBI_get_sequence(
    operation="fetch_sequence",
    accession="NC_045512.2",
    format="fasta"
)

print(genome["data"][:200])  # Preview
```

## Example 4: Compare RefSeq vs GenBank

```python
# Search returns both types
result = tu.tools.NCBI_search_nucleotide(
    operation="search",
    organism="Escherichia coli",
    strain="K-12",
    limit=5
)

accessions = tu.tools.NCBI_fetch_accessions(
    operation="fetch_accession",
    uids=result["data"]["uids"]
)

# Categorize
refseq = [a for a in accessions["data"] if a.startswith("NC_")]
genbank = [a for a in accessions["data"] if not a.startswith("NC_")]

print(f"RefSeq (NCBI only): {refseq}")
print(f"GenBank (ENA compatible): {genbank}")
```

## Example 5: Multi-Format Retrieval

```python
accessio