feat: Add DNA and RNA search functionality #105
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- Add NCBISearch searcher for DNA/GenBank/Entrez database search - Add RNACentralSearch searcher for RNA database search - Update search_all.py to support ncbi and rnacentral data sources - Add search configs for DNA, RNA, and protein (renamed from search_config) - Add search scripts for DNA and RNA - Add demo input files for DNA and RNA search - Update search_uniprot.sh to use search_protein_config.yaml This PR extends the search functionality to support biological data types: - Protein search (existing, now explicitly named) - DNA search via NCBI - RNA search via RNAcentral
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- Remove all trailing whitespace - Fix line-too-long issues (split long lines) - Remove trailing newlines at end of files - Remove unnecessary else/elif after return statements
…Gen into feat/add-dna-rna-search
- Extract utility functions (_gene_record_to_dict, _accession_to_dict, _rna_data_to_dict) - Unify method naming: search_by_keyword -> get_best_hit - Add threshold parameter to NCBI and RNAcentral searchers for interface consistency - Improve error handling with network error detection and fallback strategies - Fix RNAcentral sequence search to prioritize exact matches - Add search_rna_demo.jsonl example file
…Gen into feat/add-dna-rna-search
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- Refactor search_by_sequence in ncbi_searcher.py to reduce return statements from 7 to 1 - Refactor search_by_sequence in rnacentral_searcher.py to reduce return statements from 8 to 1 and branches from 16 to 12 - Extract helper methods to improve code readability and maintainability - Fix pylint errors R0911 (too-many-return-statements) and R0912 (too-many-branches)
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This PR extends the search functionality to support biological data types: