debase 0.1.9__py3-none-any.whl → 0.1.16__py3-none-any.whl

{debase-0.1.9.dist-info → debase-0.1.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: debase
-Version: 0.1.9
+Version: 0.1.16
 Summary: Enzyme lineage analysis and sequence extraction package
 Home-page: https://github.com/YuemingLong/DEBase
 Author: DEBase Team

debase-0.1.16.dist-info/RECORD

@@ -0,0 +1,16 @@
+debase/__init__.py,sha256=YeKveGj_8fwuu5ozoK2mUU86so_FjiCwsvg1d_lYVZU,586
+debase/__main__.py,sha256=LbxYt2x9TG5Ced7LpzzX_8gkWyXeZSlVHzqHfqAiPwQ,160
+debase/_version.py,sha256=l25FRqoNjxB5d3qBHsLMMA_9YWsIZ7nJ5BiTLj0qYE8,50
+debase/build_db.py,sha256=bW574GxsL1BJtDwM19urLbciPcejLzfraXZPpzm09FQ,7167
+debase/cleanup_sequence.py,sha256=QyhUqvTBVFTGM7ebAHmP3tif3Jq-8hvoLApYwAJtpH4,32702
+debase/enzyme_lineage_extractor.py,sha256=jNxNCh8VF0dUFxUlTall0w1-oQojXRXLnWcuPFs5ij8,106879
+debase/lineage_format.py,sha256=mACni9M1RXA_1tIyDZJpStQoutd_HLG2qQMAORTusZs,30045
+debase/reaction_info_extractor.py,sha256=9DkEZh7TgsxKpFkKbLyUhS_w0Z84LczkDFv-v_NEHE4,112174
+debase/substrate_scope_extractor.py,sha256=9XDF-DxOqB63AwaVceAMvg7BcjoTQXE_pG2c_seM_DA,100698
+debase/wrapper.py,sha256=lTx375a57EVuXcZ_roXaj5UDj8HjRcb5ViNaSgPN4Ik,10352
+debase-0.1.16.dist-info/licenses/LICENSE,sha256=5sk9_tcNmr1r2iMIUAiioBo7wo38u8BrPlO7f0seqgE,1075
+debase-0.1.16.dist-info/METADATA,sha256=7sv2OcIuHaoOImkBdoEtRzyOjp9Kuoz2ZmgK4tosaUc,10790
+debase-0.1.16.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+debase-0.1.16.dist-info/entry_points.txt,sha256=hUcxA1b4xORu-HHBFTe9u2KTdbxPzt0dwz95_6JNe9M,48
+debase-0.1.16.dist-info/top_level.txt,sha256=2BUeq-4kmQr0Rhl06AnRzmmZNs8WzBRK9OcJehkcdk8,7
+debase-0.1.16.dist-info/RECORD,,

debase/PIPELINE_FLOW.md

@@ -1,100 +0,0 @@
-# DEBase Pipeline Flow
-
-## Overview
-The DEBase pipeline extracts enzyme engineering data from chemistry papers through a series of modular steps.
-
-## Pipeline Architecture
-
-```
-┌─────────────────────┐     ┌─────────────────────┐
-│   Manuscript PDF    │     │       SI PDF        │
-└──────────┬──────────┘     └──────────┬──────────┘
-           │                           │
-           └───────────┬───────────────┘
-                       │
-                       ▼
-         ┌─────────────────────────────┐
-         │ 1. enzyme_lineage_extractor │
-         │   - Extract enzyme variants │
-         │   - Parse mutations         │
-         │   - Get basic metadata      │
-         └─────────────┬───────────────┘
-                       │
-                       ▼
-         ┌─────────────────────────────┐
-         │    2. cleanup_sequence      │
-         │   - Validate sequences      │
-         │   - Fix formatting issues   │
-         │   - Generate full sequences │
-         └─────────────┬───────────────┘
-                       │
-           ┌───────────┴───────────────┐
-           │                           │
-           ▼                           ▼
-┌─────────────────────────┐ ┌─────────────────────────┐
-│ 3a. reaction_info       │ │ 3b. substrate_scope     │
-│     _extractor          │ │     _extractor          │
-│ - Performance metrics   │ │ - Substrate variations  │
-│ - Model reaction        │ │ - Additional variants   │
-│ - Conditions            │ │ - Scope data            │
-└───────────┬─────────────┘ └───────────┬─────────────┘
-            │                           │
-            └───────────┬───────────────┘
-                        │
-                        ▼
-          ┌─────────────────────────────┐
-          │    4. lineage_format_o3     │
-          │   - Merge all data          │
-          │   - Fill missing sequences  │
-          │   - Format final output     │
-          └─────────────┬───────────────┘
-                        │
-                        ▼
-                ┌─────────────┐
-                │ Final CSV   │
-                └─────────────┘
-```
-
-## Module Details
-
-### 1. enzyme_lineage_extractor.py
-- **Input**: Manuscript PDF, SI PDF
-- **Output**: CSV with enzyme variants and mutations
-- **Function**: Extracts enzyme identifiers, mutation lists, and basic metadata
-
-### 2. cleanup_sequence.py  
-- **Input**: Enzyme lineage CSV
-- **Output**: CSV with validated sequences
-- **Function**: Validates protein sequences, generates full sequences from mutations
-
-### 3a. reaction_info_extractor.py
-- **Input**: PDFs + cleaned enzyme CSV
-- **Output**: CSV with reaction performance data
-- **Function**: Extracts yield, TTN, selectivity, reaction conditions
-
-### 3b. substrate_scope_extractor.py
-- **Input**: PDFs + cleaned enzyme CSV  
-- **Output**: CSV with substrate scope entries
-- **Function**: Extracts substrate variations tested with different enzymes
-
-### 4. lineage_format_o3.py
-- **Input**: Reaction CSV + Substrate scope CSV
-- **Output**: Final formatted CSV
-- **Function**: Merges data, fills missing sequences, applies consistent formatting
-
-## Key Features
-
-1. **Modular Design**: Each step can be run independently
-2. **Parallel Extraction**: Steps 3a and 3b run independently 
-3. **Error Recovery**: Pipeline can resume from any step
-4. **Clean Interfaces**: Each module has well-defined inputs/outputs
-
-## Usage
-
-```bash
-# Full pipeline
-python -m debase.wrapper_clean manuscript.pdf --si si.pdf --output results.csv
-
-# With intermediate files kept for debugging  
-python -m debase.wrapper_clean manuscript.pdf --si si.pdf --keep-intermediates
-```

debase-0.1.9.dist-info/RECORD

@@ -1,17 +0,0 @@
-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=j8HFA4JhFiintNU67gau8Re8N3rsxPqodcW8xAgdwqY,49
-debase/build_db.py,sha256=bW574GxsL1BJtDwM19urLbciPcejLzfraXZPpzm09FQ,7167
-debase/cleanup_sequence.py,sha256=QyhUqvTBVFTGM7ebAHmP3tif3Jq-8hvoLApYwAJtpH4,32702
-debase/enzyme_lineage_extractor.py,sha256=mHKo6cxQdcAFuthQTpxc4fsGH73JO3VuLXSsixA7mOA,97421
-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-0.1.9.dist-info/licenses/LICENSE,sha256=5sk9_tcNmr1r2iMIUAiioBo7wo38u8BrPlO7f0seqgE,1075
-debase-0.1.9.dist-info/METADATA,sha256=QVjGEYd1VWDmQszko8IQ5jJ9xMQoT45SCY_oG9XvbMs,10789
-debase-0.1.9.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-debase-0.1.9.dist-info/entry_points.txt,sha256=hUcxA1b4xORu-HHBFTe9u2KTdbxPzt0dwz95_6JNe9M,48
-debase-0.1.9.dist-info/top_level.txt,sha256=2BUeq-4kmQr0Rhl06AnRzmmZNs8WzBRK9OcJehkcdk8,7
-debase-0.1.9.dist-info/RECORD,,