debase 0.1.3__py3-none-any.whl → 0.1.4__py3-none-any.whl

debase/_version.py

@@ -1,3 +1,3 @@
 """Version information."""
 
-__version__ = "0.1.3"
+__version__ = "0.1.4"

debase/enzyme_lineage_extractor.py

@@ -800,15 +800,36 @@ def identify_evolution_locations(
                         _dump(f"=== CAMPAIGN MAPPING PROMPT ===\nLocation: {location_str}\n{'='*80}\n\n{mapping_prompt}", mapping_file)
                     
                     response = model.generate_content(mapping_prompt)
-                    campaign_id = _extract_text(response).strip().strip('"')
+                    response_text = _extract_text(response).strip()
+                    
+                    # Extract just the campaign_id from the response
+                    # Look for the campaign_id pattern in the response
+                    campaign_id = None
+                    for campaign in campaigns:
+                        if hasattr(campaign, 'campaign_id') and campaign.campaign_id in response_text:
+                            campaign_id = campaign.campaign_id
+                            break
+                    
+                    # If not found, try to extract the last line or quoted string
+                    if not campaign_id:
+                        # Try to find quoted string
+                        quoted_match = re.search(r'"([^"]+)"', response_text)
+                        if quoted_match:
+                            campaign_id = quoted_match.group(1)
+                        else:
+                            # Take the last non-empty line
+                            lines = [line.strip() for line in response_text.split('\n') if line.strip()]
+                            if lines:
+                                campaign_id = lines[-1].strip('"')
                     
                     # Save mapping response to debug if provided
                     if debug_dir:
                         response_file = debug_path / f"campaign_mapping_response_{location_str.replace(' ', '_')}_{int(time.time())}.txt"
-                        _dump(f"=== CAMPAIGN MAPPING RESPONSE ===\nLocation: {location_str}\nMapped to: {campaign_id}\n{'='*80}\n\n{_extract_text(response)}", response_file)
+                        _dump(f"=== CAMPAIGN MAPPING RESPONSE ===\nLocation: {location_str}\nFull response:\n{response_text}\nExtracted campaign_id: {campaign_id}\n{'='*80}", response_file)
                     
                     # Add campaign_id to location
-                    loc['campaign_id'] = campaign_id
+                    if campaign_id:
+                        loc['campaign_id'] = campaign_id
                     log.info(f"Mapped {location_str} to campaign: {campaign_id}")
                 except Exception as exc:
                     log.warning(f"Failed to map location to campaign: {exc}")
@@ -2038,8 +2059,15 @@ def run_pipeline(
     sequences = get_sequences(full_text, model, pdf_paths=pdf_paths, debug_dir=debug_dir)
     
     # 4a. Try PDB extraction if no sequences found -----------------------------
-    if not sequences or all(s.aa_seq is None for s in sequences):
-        log.info("No sequences found in paper, attempting PDB extraction...")
+    # Check if we need PDB sequences (no sequences or only partial sequences)
+    MIN_PROTEIN_LENGTH = 50  # Most proteins are >50 AA
+    needs_pdb = (not sequences or 
+                 all(s.aa_seq is None or (s.aa_seq and len(s.aa_seq) < MIN_PROTEIN_LENGTH) 
+                     for s in sequences))
+    
+    if needs_pdb:
+        log.info("No full-length sequences found in paper (only partial sequences < %d AA), attempting PDB extraction...", 
+                 MIN_PROTEIN_LENGTH)
         
         # Extract PDB IDs from all PDFs
         pdb_ids = []

{debase-0.1.3.dist-info → debase-0.1.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: debase
-Version: 0.1.3
+Version: 0.1.4
 Summary: Enzyme lineage analysis and sequence extraction package
 Home-page: https://github.com/YuemingLong/DEBase
 Author: DEBase Team
@@ -61,14 +61,70 @@ Enzyme lineage analysis and sequence extraction package with advanced parallel p
 
 ## Installation
 
+### Quick Install (PyPI)
 ```bash
 pip install debase
 ```
+
+### Development Setup with Conda (Recommended)
+
+1. **Clone the repository**
+```bash
+git clone https://github.com/YuemingLong/DEBase.git
+cd DEBase
+```
+
+2. **Create conda environment from provided file**
+```bash
+conda env create -f environment.yml
+conda activate debase
+```
+
+3. **Install DEBase in development mode**
+```bash
+pip install -e .
+```
+
+### Manual Setup
+
+If you prefer to set up the environment manually:
+
+```bash
+# Create new conda environment
+conda create -n debase python=3.9
+conda activate debase
+
+# Install conda packages
+conda install -c conda-forge pandas numpy matplotlib seaborn jupyter jupyterlab openpyxl biopython requests tqdm
+
+# Install RDKit (optional - used for SMILES canonicalization)
+conda install -c conda-forge rdkit
+
+# Install pip-only packages
+pip install PyMuPDF google-generativeai debase
+```
+
+**Note about RDKit**: RDKit is optional and only used for canonicalizing SMILES strings in the output. If not installed, DEBase will still function normally but SMILES strings won't be standardized.
+
 ## Requirements
 
 - Python 3.8 or higher
 - A Gemini API key (set as environment variable `GEMINI_API_KEY`)
 
+### Setting up Gemini API Key
+
+```bash
+# Option 1: Export in your shell
+export GEMINI_API_KEY="your-api-key-here"
+
+# Option 2: Add to ~/.bashrc or ~/.zshrc for persistence
+echo 'export GEMINI_API_KEY="your-api-key-here"' >> ~/.bashrc
+source ~/.bashrc
+
+# Option 3: Create .env file in project directory
+echo 'GEMINI_API_KEY=your-api-key-here' > .env
+```
+
 ## Recent Updates
 
 - **Campaign-Aware Extraction**: Automatically detects and processes multiple directed evolution campaigns in a single paper

{debase-0.1.3.dist-info → debase-0.1.4.dist-info}/RECORD

@@ -1,17 +1,17 @@
 debase/PIPELINE_FLOW.md,sha256=S4nQyZlX39-Bchw1gQWPK60sHiFpB1eWHqo5GR9oTY8,4741
 debase/__init__.py,sha256=YeKveGj_8fwuu5ozoK2mUU86so_FjiCwsvg1d_lYVZU,586
 debase/__main__.py,sha256=LbxYt2x9TG5Ced7LpzzX_8gkWyXeZSlVHzqHfqAiPwQ,160
-debase/_version.py,sha256=92QgGO0ZoG0AhULGdcMTX2RSEJkv8UZrDw2peYQOh4U,49
+debase/_version.py,sha256=mcDHWqAxAKwMNAAyHmpWVDTK-zafQ1kQjmiwnsZbUD4,49
 debase/build_db.py,sha256=bW574GxsL1BJtDwM19urLbciPcejLzfraXZPpzm09FQ,7167
 debase/cleanup_sequence.py,sha256=QyhUqvTBVFTGM7ebAHmP3tif3Jq-8hvoLApYwAJtpH4,32702
-debase/enzyme_lineage_extractor.py,sha256=sJ9Lz7Usse5NqdoZatoOEDMwbMYEgNH1HCLIGS9avn8,87774
+debase/enzyme_lineage_extractor.py,sha256=s1kPOomvJjfMSN5odxeyXNmxiaOzXyOZICr4YUWU6j8,89288
 debase/lineage_format.py,sha256=mACni9M1RXA_1tIyDZJpStQoutd_HLG2qQMAORTusZs,30045
 debase/reaction_info_extractor.py,sha256=6wWj4IyUNSugNjxpwMGjABSAp68yHABaz_7ZRjh9GEk,112162
 debase/substrate_scope_extractor.py,sha256=dbve8q3K7ggA3A6EwB-KK9L19BnMNgPZMZ05G937dSY,82262
 debase/wrapper.py,sha256=lTx375a57EVuXcZ_roXaj5UDj8HjRcb5ViNaSgPN4Ik,10352
-debase-0.1.3.dist-info/licenses/LICENSE,sha256=5sk9_tcNmr1r2iMIUAiioBo7wo38u8BrPlO7f0seqgE,1075
-debase-0.1.3.dist-info/METADATA,sha256=WUJha43ZPKgGDNZD1DYu8CfJwxUOj09kzuPSqfwe96s,9382
-debase-0.1.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-debase-0.1.3.dist-info/entry_points.txt,sha256=hUcxA1b4xORu-HHBFTe9u2KTdbxPzt0dwz95_6JNe9M,48
-debase-0.1.3.dist-info/top_level.txt,sha256=2BUeq-4kmQr0Rhl06AnRzmmZNs8WzBRK9OcJehkcdk8,7
-debase-0.1.3.dist-info/RECORD,,
+debase-0.1.4.dist-info/licenses/LICENSE,sha256=5sk9_tcNmr1r2iMIUAiioBo7wo38u8BrPlO7f0seqgE,1075
+debase-0.1.4.dist-info/METADATA,sha256=fZwXCP1i1s0VNq7Ds5bd2ys3pONgaV1XCe_edUkQdRU,10789
+debase-0.1.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+debase-0.1.4.dist-info/entry_points.txt,sha256=hUcxA1b4xORu-HHBFTe9u2KTdbxPzt0dwz95_6JNe9M,48
+debase-0.1.4.dist-info/top_level.txt,sha256=2BUeq-4kmQr0Rhl06AnRzmmZNs8WzBRK9OcJehkcdk8,7
+debase-0.1.4.dist-info/RECORD,,