Merge pull request #105 from CHERRY-ui8/feat/add-dna-rna-search

feat: Add DNA and RNA search functionality

Author: CHERRY-ui8

graphgen/configs/search_config.yaml

@@ -0,0 +1,17 @@
+pipeline:
+  - name: read_step
+    op_key: read
+    params:
+      input_file:  resources/input_examples/search_dna_demo.jsonl # input file path, support json, jsonl, txt, pdf. See resources/input_examples for examples
+
+  - name: search_step
+    op_key: search
+    deps: [read_step] # search_step depends on read_step
+    params:
+      data_sources: [ncbi] # data source for searcher, support: wikipedia, google, uniprot, ncbi, rnacentral
+      ncbi_params:
+        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)
+

graphgen/configs/search_dna_config.yaml

@@ -0,0 +1,15 @@
+pipeline:
+  - name: read_step
+    op_key: read
+    params:
+      input_file:  resources/input_examples/search_protein_demo.jsonl # input file path, support json, jsonl, txt, pdf. See resources/input_examples for examples
+
+  - name: search_step
+    op_key: search
+    deps: [read_step] # search_step depends on read_step
+    params:
+      data_sources: [uniprot] # data source for searcher, support: wikipedia, google, uniprot
+      uniprot_params:
+        use_local_blast: true # whether to use local blast for uniprot search
+        local_blast_db: /your_path/2024_01/uniprot_sprot # format: /path/to/${RELEASE}/uniprot_sprot
+        # options: uniprot_sprot (recommended, high quality), uniprot_trembl, or uniprot_${RELEASE} (merged database)

graphgen/configs/search_protein_config.yaml

@@ -0,0 +1,16 @@
+pipeline:
+  - name: read_step
+    op_key: read
+    params:
+      input_file:  resources/input_examples/search_rna_demo.jsonl # input file path, support json, jsonl, txt, pdf. See resources/input_examples for examples
+
+  - name: search_step
+    op_key: search
+    deps: [read_step] # search_step depends on read_step
+    params:
+      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)
+

graphgen/configs/search_rna_config.yaml

@@ -45,7 +45,7 @@ def __init__(
 
         # llm
         self.tokenizer_instance: Tokenizer = tokenizer_instance or Tokenizer(
-            model_name=os.getenv("TOKENIZER_MODEL")
+            model_name=os.getenv("TOKENIZER_MODEL", "cl100k_base")
         )
 
         self.synthesizer_llm_client: BaseLLMWrapper = (

graphgen/graphgen.py

@@ -26,6 +26,8 @@
     RDFReader,
     TXTReader,
 )
+from .searcher.db.ncbi_searcher import NCBISearch
+from .searcher.db.rnacentral_searcher import RNACentralSearch
 from .searcher.db.uniprot_searcher import UniProtSearch
 from .searcher.kg.wiki_search import WikiSearch
 from .searcher.web.bing_search import BingSearch