fix: fix dna/rna local blast

.gitignore

@@ -177,3 +177,7 @@ cache
 *.pyc
 *.html
 .gradio
+
+# macOS
+.DS_Store
+**/.DS_Store

graphgen/configs/search_dna_config.yaml

@@ -13,5 +13,5 @@ pipeline:
         email: [email protected] # NCBI requires an email address
         tool: GraphGen # tool name for NCBI API
         use_local_blast: true # whether to use local blast for DNA search
-        local_blast_db: /your_path/refseq_241 # path to local BLAST database (without .nhr extension)
+        local_blast_db: refseq_release/refseq_release # path to local BLAST database (without .nhr extension)
 

graphgen/configs/search_rna_config.yaml

@@ -11,6 +11,4 @@ pipeline:
       data_sources: [rnacentral] # data source for searcher, support: wikipedia, google, uniprot, ncbi, rnacentral
       rnacentral_params:
         use_local_blast: true # whether to use local blast for RNA search
-        local_blast_db: /your_path/refseq_rna_241 # format: /path/to/refseq_rna_${RELEASE}
-        # can also use DNA database with RNA sequences (if already built)
-
+        local_blast_db: rnacentral_ensembl_gencode_YYYYMMDD/ensembl_gencode_YYYYMMDD # path to local BLAST database (without .nhr extension)

graphgen/models/searcher/db/ncbi_searcher.py

@@ -83,6 +83,29 @@ def _nested_get(data: dict, *keys, default=None):
             data = data.get(key, default)
         return data
 
+    @staticmethod
+    def _infer_molecule_type_detail(accession: Optional[str], gene_type: Optional[int] = None) -> Optional[str]:
+        """Infer molecule_type_detail from accession prefix or gene type."""
+        if accession:
+            if accession.startswith(("NM_", "XM_")):
+                return "mRNA"
+            if accession.startswith(("NC_", "NT_")):
+                return "genomic DNA"
+            if accession.startswith(("NR_", "XR_")):
+                return "RNA"
+            if accession.startswith("NG_"):
+                return "genomic region"
+        # Fallback: infer from gene type if available
+        if gene_type is not None:
+            gene_type_map = {
+                3: "rRNA",
+                4: "tRNA",
+                5: "snRNA",
+                6: "ncRNA",
+            }
+            return gene_type_map.get(gene_type)
+        return None
+
     def _gene_record_to_dict(self, gene_record, gene_id: str) -> dict:
         """
         Convert an Entrez gene record to a dictionary.
@@ -120,7 +143,7 @@ def _gene_record_to_dict(self, gene_record, gene_id: str) -> dict:
             else None
         )
 
-        # Extract representative accession
+        # Extract representative accession (prefer type 3 = mRNA/transcript)
         representative_accession = next(
             (
                 product.get("Gene-commentary_accession")
@@ -129,6 +152,17 @@ def _gene_record_to_dict(self, gene_record, gene_id: str) -> dict:
             ),
             None,
         )
+        # Fallback: if no type 3 accession, try any available accession
+        # This is needed for genes that don't have mRNA transcripts but have other sequence records
+        if not representative_accession:
+            representative_accession = next(
+                (
+                    product.get("Gene-commentary_accession")
+                    for product in locus.get("Gene-commentary_products", [])
+                    if product.get("Gene-commentary_accession")
+                ),
+                None,
+            )
 
         # Extract function
         function = data.get("Entrezgene_summary") or next(
@@ -169,18 +203,19 @@ def _gene_record_to_dict(self, gene_record, gene_id: str) -> dict:
             "sequence": None,
             "sequence_length": None,
             "gene_id": gene_id,
-            "molecule_type_detail": None,
+            "molecule_type_detail": self._infer_molecule_type_detail(
+                representative_accession, data.get("Entrezgene_type")
+            ),
             "_representative_accession": representative_accession,
         }
 
     def get_by_gene_id(self, gene_id: str, preferred_accession: Optional[str] = None) -> Optional[dict]:
         """Get gene information by Gene ID."""
-        def _extract_from_genbank(result: dict, accession: str):
-            """Enrich result dictionary with sequence and summary information from accession."""
+        def _extract_metadata_from_genbank(result: dict, accession: str):
+            """Extract metadata from GenBank format (title, features, organism, etc.)."""
             with Entrez.efetch(db="nuccore", id=accession, rettype="gb", retmode="text") as handle:
                 record = SeqIO.read(handle, "genbank")
-                result["sequence"] = str(record.seq)
-                result["sequence_length"] = len(record.seq)
+
                 result["title"] = record.description
                 result["molecule_type_detail"] = (
                     "mRNA" if accession.startswith(("NM_", "XM_")) else
@@ -206,6 +241,22 @@ def _extract_from_genbank(result: dict, accession: str):
 
             return result
 
+        def _extract_sequence_from_fasta(result: dict, accession: str):
+            """Extract sequence from FASTA format (more reliable than GenBank for CON-type records)."""
+            try:
+                with Entrez.efetch(db="nuccore", id=accession, rettype="fasta", retmode="text") as fasta_handle:
+                    fasta_record = SeqIO.read(fasta_handle, "fasta")
+                    result["sequence"] = str(fasta_record.seq)
+                    result["sequence_length"] = len(fasta_record.seq)
+            except Exception as fasta_exc:
+                logger.warning(
+                    "Failed to extract sequence from accession %s using FASTA format: %s",
+                    accession, fasta_exc
+                )
+                result["sequence"] = None
+                result["sequence_length"] = None
+            return result
+
         try:
             with Entrez.efetch(db="gene", id=gene_id, retmode="xml") as handle:
                 gene_record = Entrez.read(handle)
@@ -214,7 +265,8 @@ def _extract_from_genbank(result: dict, accession: str):
 
                 result = self._gene_record_to_dict(gene_record, gene_id)
                 if accession := (preferred_accession or result.get("_representative_accession")):
-                    result = _extract_from_genbank(result, accession)
+                    result = _extract_metadata_from_genbank(result, accession)
+                    result = _extract_sequence_from_fasta(result, accession)
 
                 result.pop("_representative_accession", None)
                 return result

resources/input_examples/search_dna_demo.jsonl

@@ -1,9 +1,4 @@
-{"type": "text", "content": "TP53"}
-{"type": "text", "content": "BRCA1"}
-{"type": "text", "content": "672"}
-{"type": "text", "content": "11998"}
-{"type": "text", "content": "NM_000546"}
-{"type": "text", "content": "NM_024140"}
-{"type": "text", "content": ">query\nCTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTACATGTGTAACAGTTCCTGCATGGGCGGCATGAACCGGAGGCCCATCCTCACCATCATCACACTGGAAGACTCCAGTGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCGCAAGAAAGGGGAGCCTCACCACGAGCTGCCCCCAGGGAGCACTAAGCGAGCACTGCCCAACAACACCAGCTCCTCTCCCCAGCCAAAGAAGAAACCACTGGATGGAGAATATTTCACCCTTCAGATCCGTGGGCGTGAGCGCTTCGAGATGTTCCGAGAGCTGAATGAGGCCTTGGAACTCAAGGATGCCCAGGCTGGGAAGGAGCCAGGGGGGAGCAGGGCTCACTCCAGCCACCTGAAGTCCAAAAAGGGTCAGTCTACCTCCCGCCATAAAAAACTCATGTTCAAGACAGAAGGGCCTGACTCAGACTGACATTCTCCACTTCTTGTTCCCCACTGACAGCCTCCCACCCCCATCTCTCCCTCCCCTGCCATTTTGGGTTTTGGGTCTTTGAACCCTTGCTTGCAATAGGTGTGCGTCAGAAGCACCCAGGACTTCCATTTGCTTTGTCCCGGGGCTCCACTGAACAAGTTGGCCTGCACTGGTGTTTTGTTGTGGGGAGGAGGATGGGGAGTAGGACATACCAGCTTAGATTTTAAGGTTTTTACTGTGAGGGATGTTTGGGAGATGTAAGAAATGTTCTTGCAGTTAAGGGTTAGTTTACAATCAGCCACATTCTAGGTAGGGGCCCACTTCACCGTACTAACCAGGGAAGCTGTCCCTCACTGTTGAATTTTCTCTAACTTCAAGGCCCATATCTGTGAAATGCTGGCATTTGCACCTACCTCACAGAGTGCATTGTGAGGGTTAATGAAATAATGTACATCTGGCCTTGAAACCACCTTTTATTACATGGGGTCTAGAACTTGACCCCCTTGAGGGTGCTTGTTCCCTCTCCCTGTTGGTCGGTGGGTTGGTAGTTTCTACAGTTGGGCAGCTGGTTAGGTAGAGGGAGTTGTCAAGTCTCTGCTGGCCCAGCCAAACCCTGTCTGACAACCTCTTGGTGAACCTTAGTACCTAAAAGGAAATCTCACCCCATCCCACACCCTGGAGGATTTCATCTCTTGTATATGATGATCTGGATCCACCAAGACTTGTTTTATGCTCAGGGTCAATTTCTTTTTTCTTTTTTTTTTTTTTTTTTCTTTTTCTTTGAGACTGGGTCTCGCTTTGTTGCCCAGGCTGGAGTGGAGTGGCGTGATCTTGGCTTACTGCAGCCTTTGCCTCCCCGGCTCGAGCAGTCCTGCCTCAGCCTCCGGAGTAGCTGGGACCACAGGTTCATGCCACCATGGCCAGCCAACTTTTGCATGTTTTGTAGAGATGGGGTCTCACAGTGTTGCCCAGGCTGGTCTCAAACTCCTGGGCTCAGGCGATCCACCTGTCTCAGCCTCCCAGAGTGCTGGGATTACAATTGTGAGCCACCACGTCCAGCTGGAAGGGTCAACATCTTTTACATTCTGCAAGCACATCTGCATTTTCACCCCACCCTTCCCCTCCTTCTCCCTTTTTATATCCCATTTTTATATCGATCTCTTATTTTACAATAAAACTTTGCTGCCA"}
-{"type": "text", "content": "CTCAAAAGTCTAGAGCCACCGTCCAGGGAGCAGGTAGCTGCTGGGCTCCGGGGACACTTTGCGTTCGGGCTGGGAGCGTGCTTTCCACGACGGTGACACGCTTCCCTGGATTGGCAGCCAGACTGCCTTCCGGGTCACTGCCATGGAGGAGCCGCAGTCAGATCCTAGCGTCGAGCCCCCTCTGAGTCAGGAAACATTTTCAGACCTATGGAAACTACTTCCTGAAAACAACGTTCTGTCCCCCTTGCCGTCCCAAGCAATGGATGATTTGATGCTGTCCCCGGACGATATTGAACAATGGTTCACTGAAGACCCAGGTCCAGATGAAGCTCCCAGAATGCCAGAGGCTGCTCCCCCCGTGGCCCCTGCACCAGCAGCTCCTACACCGGCGGCCCCTGCACCAGCCCCCTCCTGGCCCCTGTCATCTTCTGTCCCTTCCCAGAAAACCTACCAGGGCAGCTACGGTTTCCGTCTGGGCTTCTTGCATTCTGGGACAGCCAAGTCTGTGACTTGCACGTACTCCCCTGCCCTCAACAAGATGTTTTGCCAACTGGCCAAGACCTGCCCTGTGCAGCTGTGGGTTGATTCCACACCCCCGCCCGGCACCCGCGTCCGCGCCATGGCCATCTACAAGCAGTCACAGCACATGACGGAGGTTGTGAGGCGCTGCCCCCACCATGAGCGCTGCTCAGATAGCGATGGTCTGGCCCCTCCTCAGCATCTTATCCGAGTGGAAGGAAATTTGCGTGTGGAGTATTTGGATGACAGAAACACTTTTCGACATAGTGTGGTGGTGCCCTATGAGCCGCCTGAGGTTGGCTCTGACTGTACCACCATCCACTACAACTACATGTGTAACAGTTCCTGCATGGGCGGCATGAACCGGAGGCCCATCCTCACCATCATCACACTGGAAGACTCCAGTGGTAATCTACTGGGACGGAACAGCTTTGAGGTGCGTGTTTGTGCCTGTCCTGGGAGAGACCGGCGCACAGAGGAAGAGAATCTCCGCAAGAAAGGGGAGCCTCACCACGAGCTGCCCCCAGGGAGCACTAAGCGAGCACTGCCCAACAACACCAGCTCCTCTCCCCAGCCAAAGAAGAAACCACTGGATGGAGAATATTTCACCCTTCAGATCCGTGGGCGTGAGCGCTTCGAGATGTTCCGAGAGCTGAATGAGGCCTTGGAACTCAAGGATGCCCAGGCTGGGAAGGAGCCAGGGGGGAGCAGGGCTCACTCCAGCCACCTGAAGTCCAAAAAGGGTCAGTCTACCTCCCGCCATAAAAAACTCATGTTCAAGACAGAAGGGCCTGACTCAGACTGACATTCTCCACTTCTTGTTCCCCACTGACAGCCTCCCACCCCCATCTCTCCCTCCCCTGCCATTTTGGGTTTTGGGTCTTTGAACCCTTGCTTGCAATAGGTGTGCGTCAGAAGCACCCAGGACTTCCATTTGCTTTGTCCCGGGGCTCCACTGAACAAGTTGGCCTGCACTGGTGTTTTGTTGTGGGGAGGAGGATGGGGAGTAGGACATACCAGCTTAGATTTTAAGGTTTTTACTGTGAGGGATGTTTGGGAGATGTAAGAAATGTTCTTGCAGTTAAGGGTTAGTTTACAATCAGCCACATTCTAGGTAGGGGCCCACTTCACCGTACTAACCAGGGAAGCTGTCCCTCACTGTTGAATTTTCTCTAACTTCAAGGCCCATATCTGTGAAATGCTGGCATTTGCACCTACCTCACAGAGTGCATTGTGAGGGTTAATGAAATAATGTACATCTGGCCTTGAAACCACCTTTTATTACATGGGGTCTAGAACTTGACCCCCTTGAGGGTGCTTGTTCCCTCTCCCTGTTGGTCGGTGGGTTGGTAGTTTCTACAGTTGGGCAGCTGGTTAGGTAGAGGGAGTTGTCAAGTCTCTGCTGGCCCAGCCAAACCCTGTCTGACAACCTCTTGGTGAACCTTAGTACCTAAAAGGAAATCTCACCCCATCCCACACCCTGGAGGATTTCATCTCTTGTATATGATGATCTGGATCCACCAAGACTTGTTTTATGCTCAGGGTCAATTTCTTTTTTCTTTTTTTTTTTTTTTTTTCTTTTTCTTTGAGACTGGGTCTCGCTTTGTTGCCCAGGCTGGAGTGGAGTGGCGTGATCTTGGCTTACTGCAGCCTTTGCCTCCCCGGCTCGAGCAGTCCTGCCTCAGCCTCCGGAGTAGCTGGGACCACAGGTTCATGCCACCATGGCCAGCCAACTTTTGCATGTTTTGTAGAGATGGGGTCTCACAGTGTTGCCCAGGCTGGTCTCAAACTCCTGGGCTCAGGCGATCCACCTGTCTCAGCCTCCCAGAGTGCTGGGATTACAATTGTGAGCCACCACGTCCAGCTGGAAGGGTCAACATCTTTTACATTCTGCAAGCACATCTGCATTTTCACCCCACCCTTCCCCTCCTTCTCCCTTTTTATATCCCATTTTTATATCGATCTCTTATTTTACAATAAAACTTTGCTGCCA"}
-
+{"type": "text", "content": "NG_033923"}
+{"type": "text", "content": "NG_056118"}
+{"type": "text", "content": ">query\nACTCAATTGTCCCAGCAGCATCTACCGAAAAGCCCCCTTGCTGTTCCTGCCAACTTGAAGCCCGGAGGCCTGCTGGGAGGAGGAATTCTAAATGACAAGTATGCCTGGAAAGCTGTGGTCCAAGGCCGTTTTTGCCGTCAGCAGGATCTCCAGAACCAAAGGGAGGACACAGCTCTTCTTAAAACTGAAGGTATTTATGGCTGACATAAAATGAGATTTGATTTGGGCAGGAAATGCGCTTATGTGTACAAAGAATAATACTGACTCCTGGCAGCAAACCAAACAAAACCAGAGTAAGGTGGAGAAAGGTAACGTGTGCCCACGGAAACAGTGGCACAATGTGTGCCTAATTCCAAAGCAGCCGTCCTGCTTAGGCCACTAGTCACGGCGGCTCTGTGATGCTGTACTCCTCAAGGATTTGAACTAATGAAAAGTAAATAAATACCAGTAAAAGTGGATTTGTAAAAAGAAAAGAAAAATGATAGGAAAAGCCCCTTTACCATATGTCAAGGGTTTATGCTG"}
+{"type": "text", "content": "ACTCAATTGTCCCAGCAGCATCTACCGAAAAGCCCCCTTGCTGTTCCTGCCAACTTGAAGCCCGGAGGCCTGCTGGGAGGAGGAATTCTAAATGACAAGTATGCCTGGAAAGCTGTGGTCCAAGGCCGTTTTTGCCGTCAGCAGGATCTCCAGAACCAAAGGGAGGACACAGCTCTTCTTAAAACTGAAGGTATTTATGGCTGACATAAAATGAGATTTGATTTGGGCAGGAAATGCGCTTATGTGTACAAAGAATAATACTGACTCCTGGCAGCAAACCAAACAAAACCAGAGTAAGGTGGAGAAAGGTAACGTGTGCCCACGGAAACAGTGGCACAATGTGTGCCTAATTCCAAAGCAGCCGTCCTGCTTAGGCCACTAGTCACGGCGGCTCTGTGATGCTGTACTCCTCAAGGATTTGAACTAATGAAAAGTAAATAAATACCAGTAAAAGTGGATTTGTAAAAAGAAAAGAAAAATGATAGGAAAAGCCCCTTTACCATATGTCAAGGGTTTATGCTG"}

resources/input_examples/search_rna_demo.jsonl

@@ -1,5 +1,8 @@
 {"type": "text", "content": "hsa-let-7a-1"}
+{"type": "text", "content": "XIST regulator"}
 {"type": "text", "content": "URS0000123456"}
 {"type": "text", "content": "URS0000000001"}
+{"type": "text", "content": "URS0000000787"}
+{"type": "text", "content": "GCAGTTCTCAGCCATGACAGATGGGAGTTTCGGCCCAATTGACCAGTATTCCTTACTGATAAGAGACACTGACCATGGAGTGGTTCTGGTGAGATGACATGACCCTCGTGAAGGGGCCTGAAGCTTCATTGTGTTTGTGTATGTTTCTCTCTTCAAAAATATTCATGACTTCTCCTGTAGCTTGATAAATATGTATATTTACACACTGCA"}
 {"type": "text", "content": ">query\nCUCCUUUGACGUUAGCGGCGGACGGGUUAGUAACACGUGGGUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUCGAACCGCAUGGUUCGAUAGUGAAAGAUGGUUUUGCUAUCACUUAUAGAUGGACCCGCGCCGUAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCGACGAUACGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGGGG"}
 {"type": "text", "content": "CUCCUUUGACGUUAGCGGCGGACGGGUUAGUAACACGUGGGUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUCGAACCGCAUGGUUCGAUAGUGAAAGAUGGUUUUGCUAUCACUUAUAGAUGGACCCGCGCCGUAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCGACGAUACGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGGGG"}

scripts/search/build_db/build_dna_blast_db.sh

@@ -24,7 +24,8 @@ set -e
 #   - {category}.{number}.genomic.fna.gz (基因组序列)
 #   - {category}.{number}.rna.fna.gz (RNA序列)
 #
-# Usage: ./build_dna_blast_db.sh [representative|complete|all]
+# Usage: ./build_dna_blast_db.sh [human_mouse|representative|complete|all]
+#   human_mouse: Download only Homo sapiens and Mus musculus sequences (minimal, smallest)
 #   representative: Download genomic sequences from major categories (recommended, smaller)
 #                    Includes: vertebrate_mammalian, vertebrate_other, bacteria, archaea, fungi
 #   complete: Download all complete genomic sequences from complete/ directory (very large)
@@ -35,7 +36,7 @@ set -e
 # For CentOS/RHEL/Fedora: sudo dnf install ncbi-blast+
 # Or download from: https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
 
-DOWNLOAD_TYPE=${1:-representative}
+DOWNLOAD_TYPE=${1:-human_mouse}
 
 # Better to use a stable DOWNLOAD_TMP name to support resuming downloads
 DOWNLOAD_TMP=_downloading_dna
@@ -57,8 +58,66 @@ else
     echo "Using date as release identifier: ${RELEASE}"
 fi
 
+# Function to check if a file contains target species
+check_file_for_species() {
+    local url=$1
+    local filename=$2
+    local temp_file="/tmp/check_${filename//\//_}"
+
+    # Download first 500KB (enough to get many sequence headers)
+    # This should be sufficient to identify the species in most cases
+    if curl -s --max-time 30 --range 0-512000 "${url}" -o "${temp_file}" 2>/dev/null && [ -s "${temp_file}" ]; then
+        # Try to decompress and check for species names
+        if gunzip -c "${temp_file}" 2>/dev/null | head -2000 | grep -qE "(Homo sapiens|Mus musculus)"; then
+            rm -f "${temp_file}"
+            return 0  # Contains target species
+        else
+            rm -f "${temp_file}"
+            return 1  # Does not contain target species
+        fi
+    else
+        # If partial download fails, skip this file (don't download it)
+        rm -f "${temp_file}"
+        return 1
+    fi
+}
+
 # Download based on type
 case ${DOWNLOAD_TYPE} in
+    human_mouse)
+        echo "Downloading RefSeq sequences for Homo sapiens and Mus musculus only (minimal size)..."
+        echo "This will check each file to see if it contains human or mouse sequences..."
+        category="vertebrate_mammalian"
+        echo "Checking files in ${category} category..."
+
+        # Get list of files and save to temp file to avoid subshell issues
+        curl -s "https://ftp.ncbi.nlm.nih.gov/refseq/release/${category}/" | \
+            grep -oE 'href="[^"]*\.genomic\.fna\.gz"' | \
+            sed 's/href="\(.*\)"/\1/' > /tmp/refseq_files.txt
+
+        file_count=0
+        download_count=0
+
+        while read filename; do
+            file_count=$((file_count + 1))
+            url="https://ftp.ncbi.nlm.nih.gov/refseq/release/${category}/${filename}"
+            echo -n "[${file_count}] Checking ${filename}... "
+
+            if check_file_for_species "${url}" "${filename}"; then
+                echo "✓ contains target species, downloading..."
+                download_count=$((download_count + 1))
+                wget -c -q --show-progress "${url}" || {
+                    echo "Warning: Failed to download ${filename}"
+                }
+            else
+                echo "✗ skipping (no human/mouse data)"
+            fi
+        done < /tmp/refseq_files.txt
+
+        rm -f /tmp/refseq_files.txt
+        echo ""
+        echo "Summary: Checked ${file_count} files, downloaded ${download_count} files containing human or mouse sequences."
+        ;;
     representative)
         echo "Downloading RefSeq representative sequences (recommended, smaller size)..."
         # Download major categories for representative coverage
@@ -109,7 +168,11 @@ case ${DOWNLOAD_TYPE} in
         ;;
     *)
         echo "Error: Unknown download type '${DOWNLOAD_TYPE}'"
-        echo "Usage: $0 [representative|complete|all]"
+        echo "Usage: $0 [human_mouse|representative|complete|all]"
+        echo "  human_mouse: Download only Homo sapiens and Mus musculus (minimal)"
+        echo "  representative: Download major categories (recommended)"
+        echo "  complete: Download all complete genomic sequences (very large)"
+        echo "  all: Download all genomic sequences (extremely large)"
         echo "Note: For RNA sequences, use build_rna_blast_db.sh instead"
         exit 1
         ;;