BLAST Support

KEGGBLAST provides two ways to BLAST your newly exported FASTA files against NCBI’s “nr” database (or any other you choose):

Tool	Interface	Output Format	Taxonomic Filter	Notes
gget	Python API	JSON	❌ No	Fast setup, minimal dependencies
NCBI API	HTTP POST	JSON	✅ Yes (txid…)	Full taxonomy support, needs API key

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1. gget BLAST (no tax filter)

from keggblast.blast_gget import run_gget_blast_all
run_gget_blast_all(
    program="blastp",
    database="nr",
    query_folder="fasta_output/hsa",
    output_folder="blast_results_gget"
)

Produces one JSON file per FASTA (e.g., GENE1_blastp_blast.json).

• Pros:

  • No need for NCBI_API_KEY

  • Instant JSON response

• Cons:

  • Cannot specify txid####[ORGN] to limit hits by taxonomy

2. NCBI API BLAST (with optional tax filter)

from keggblast.blast_ncbi import run_ncbi_blast_all
run_ncbi_blast_all(
    program="blastp",
    database="nr",
    query_folder="fasta_output/hsa",
    output_folder="blast_results_ncbi",
    tax_query="txid4751[ORGN]"  # restrict to Fungi
)

• Produces one JSON per FASTA.

• Pros:

  • Can do txid4751[ORGN], txid9606[ORGN], etc.

  • Official NCBI endpoints (more stable)

• Cons:

  • Requires export NCBI_API_KEY=… for high throughput

  • Slightly more setup (XML parsing vs. JSON)