AdvancedAnalysisFileParser 0.1.0__py3-none-any.whl

AdvancedAnalysisFileParser/advConfig.json

@@ -0,0 +1,96 @@
+{
+    "LPA": {
+        "Warning": null
+    },
+    "SMN": {
+        "Warning": {
+            "type": "smn",
+            "caller_name": "SMN Caller",
+            "disease_name": "Spinal Muscular Atrophy",
+            "silent_carrier_variant": "NM_000344.4:c.*3+80T>G",
+            "silent_carrier_min_allele_copy": 1
+        }
+    },
+    "HBA": {
+        "Warning": {
+            "type": "genotype",
+            "caller_name": "HBA Special Caller",
+            "genotype_data_key": "genotype",
+            "phenotypeGenotypeMapping": {
+                "normal": ["aa/aa"],
+                "carrier": [
+                    "--/aaa3.7",
+                    "--/aaa4.2",
+                    "-a3.7/-a3.7",
+                    "-a4.2/-a4.2",
+                    "-a3.7/-a4.2",
+                    "--/aa",
+                    "-a20.5/-a20.5",
+                    "-a20.5/-a3.7",
+                    "-a20.5/-a4.2",
+                    "--/aaa20.5"
+                ],
+                "silent carrier": [
+                    "-a3.7/aa",
+                    "-a4.2/aa",
+                    "-a20.5/aa"
+                ],
+                "positive for hemoglobin Bart's hydrops fetalis disease": ["--/--"],
+                "positive for hemoglobin H disease": [
+                    "--/-a3.7",
+                    "--/-a4.2",
+                    "--/-a20.5"
+                ]
+            },
+            "genotypeReference": [
+                "aaa3.7/aa",
+                "aaa4.2/aa",
+                "aaa20.5/aa",
+                "aaa20.5/aaa3.7",
+                "aaa20.5/aaa4.2",
+                "aaa20.5/aaa20.5",
+                "aa/aa",
+                "-a3.7/aa",
+                "-a4.2/aa",
+                "-a20.5/aa",
+                "--/aaa3.7",
+                "--/aaa4.2",
+                "--/aaa20.5",
+                "-a3.7/aaa20.5",
+                "-a4.2/aaa20.5",
+                "-a20.5/aaa3.7",
+                "-a20.5/aaa4.2",
+                "-a3.7/-a3.7",
+                "-a4.2/-a4.2",
+                "-a20.5/-a20.5",
+                "-a3.7/-a4.2",
+                "-a20.5/-a3.7",
+                "-a20.5/-a4.2",
+                "--/aa",
+                "--/-a3.7",
+                "--/-a4.2",
+                "--/-a20.5",
+                "--/--"
+            ]
+        }
+    },
+    "RH": {
+        "Warning": null
+    },
+    "CYP2D6": {
+        "Warning": null
+    },
+    "CYP2B6": {
+        "Warning": null
+    },
+    "CYP21A2": {
+        "Warning": null
+    },
+    "GBA": {
+        "Warning": {
+            "type": "gba",
+            "caller_name": "GBA Caller",
+            "disease_name": "Gaucher disease"
+        }
+    }
+}

AdvancedAnalysisFileParser/dragen_500_tsv_config.json

@@ -0,0 +1,53 @@
+{
+    "MSI": {
+        "caller_name": "Percent Unstable MSI Sites",
+        "fields":{
+            "Usable MSI Sites":{
+                "Warning":{
+                    "type": "condition",
+                    "conditions":[
+                        {
+                            "operator": "GT",
+                            "value": 10,
+                            "message": "MSI>10 detected in this sample"
+                        }
+                    ]
+                }
+            }
+        }
+    },
+    "TMB": {
+        "caller_name": "Total TMB",
+        "fields":{
+            "Total TMB":{
+                "Warning":{
+                    "type": "condition",
+                    "conditions":[
+                        {
+                            "operator": "GT",
+                            "value": 10,
+                            "message": "TMB>10 detected in this sample"
+                        }
+                    ]
+                }
+            }
+        }
+    },
+    "GIS": {
+        "caller_name": "Genomic Instability Score",
+        "fields":{
+            "Genomic Instability Score":{
+                "Warning": {
+                    "type": "condition",
+                    "conditions": [
+                        {
+                            "operator": "GT",
+                            "value": 42,
+                            "message": "GIS>42 detected in this sample"
+                        }
+                    ]
+                }
+            }
+        }
+    }
+}

AdvancedAnalysisFileParser/gba_tsv_config.json

@@ -0,0 +1,23 @@
+{
+    "GBA": {
+        "caller_name": "GBA Special Caller",
+        "Warning": {
+            "type": "condition",
+            "disease_name": "Gaucher disease",
+            "conditions": [
+                {
+                    "field": "is_carrier",
+                    "value": true,
+                    "operator": "EQ",
+                    "message": "Based on the GBA Caller, this sample is positive for Gaucher disease"
+                },
+                {
+                    "field": "is_biallelic",
+                    "value": true,
+                    "operator": "EQ",
+                    "message": "Based on the GBA Caller, this sample is positive for Gaucher disease"
+                }
+            ]
+        }
+    }
+}

AdvancedAnalysisFileParser/run_test_parser.py

@@ -0,0 +1,29 @@
+import json
+import os
+import sys
+
+# Ensure package import works when running this file directly
+CURRENT_DIR = os.path.dirname(__file__)
+PARENT_DIR = os.path.dirname(CURRENT_DIR)
+if PARENT_DIR not in sys.path:
+    sys.path.insert(0, PARENT_DIR)
+
+from AdvancedAnalysisFileParser import AdvancedAnalysisParser
+
+def main():
+    base = os.path.join(os.path.dirname(__file__), "Test")
+    filename = "gba_positive_1.json"
+    request = {
+        "input_dir": base,
+        "output_dir": base,
+        "output_json": "adv_output.json",
+        "map_files": {
+            filename: {}
+        }
+    }
+    parser = AdvancedAnalysisParser(request)
+    result = parser.run(return_dict=True)
+    print(json.dumps(result, indent=2))
+
+if __name__ == "__main__":
+    main()

AdvancedAnalysisFileParser/smn_tsv_config.json

@@ -0,0 +1,23 @@
+{
+    "SMN1": {
+        "caller_name": "SMN Special Caller",
+        "Warning": {
+            "type": "condition",
+            "disease_name": "Spinal Muscular Atrophy",
+            "conditions": [
+                {
+                    "field": "isSMA",
+                    "value": true,
+                    "operator": "EQ",
+                    "message": "Based on the SMN Caller, this sample is positive for Spinal Muscular Atrophy"
+                },
+                {
+                    "field": "isCarrier",
+                    "value": true,
+                    "operator": "EQ",
+                    "message": "Based on the SMN Caller, this sample is positive for Spinal Muscular Atrophy"
+                }
+            ]
+        }
+    }
+}

advancedanalysisfileparser-0.1.0.dist-info/METADATA

@@ -0,0 +1,152 @@
+Metadata-Version: 2.4
+Name: AdvancedAnalysisFileParser
+Version: 0.1.0
+Summary: Parse Illumina-DRAGEN TSV/JSON outputs to unified geneyx         JSON with warnings.
+Author: Bar Cohen
+Author-email: Bar Cohen <bar@geneyx.com>
+License: MIT License
+        
+        Copyright (c) 2026 Geneyx
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Dynamic: license-file
+
+
+
+# AdvancedAnalysisFileParser
+
+![PyPI version](https://img.shields.io/pypi/v/AdvancedAnalysisFileParser.svg?label=PyPI%20version)
+
+A Python package to parse Illumina-DRAGEN "special caller" outputs (TSV/JSON) into a unified JSON format, with automatic warnings based on user-defined or default conditions. Supports oncology, GBA, SMN, HBA, and more.
+
+---
+
+## Features
+
+- Unified JSON output for multiple DRAGEN caller types (TSV/JSON)
+- Automatic warnings for each file type, based on config or defaults
+- Pluggable parser architecture for new file types
+- CLI and Python API usage
+- Example configs and test data included
+
+---
+
+## Installation
+
+Install from PyPI (recommended):
+
+```bash
+pip install AdvancedAnalysisFileParser
+```
+
+Or from source:
+
+```bash
+git clone https://github.com/geneyx/geneyx.analysis.api.git
+cd geneyx.analysis.api/scripts/AdvancedAnalysisFileParser
+pip install -e .
+```
+
+---
+
+## Quickstart
+
+### Python API Usage
+
+```python
+from AdvancedAnalysisFileParser.AdvancedAnalysisParser import AdvancedAnalysisParser
+
+request = {
+		"input_dir": "./Test",
+		"output_dir": "./Test",
+		"output_json": "adv_output.json",
+		# Optionally, you can specify input_files or map_files for custom configs
+}
+parser = AdvancedAnalysisParser(request)
+parser.run()  # writes output to adv_output.json
+
+# Or get result as dict:
+result = parser.run(return_dict=True)
+print(result)
+```
+
+### Command-Line Usage
+
+Create a config file (e.g. `config.json`):
+
+```json
+{
+	"input_dir": "./Test",
+	"output_dir": "./Test",
+	"output_json": "adv_output.json"
+}
+```
+
+Then run:
+
+```bash
+python -m AdvancedAnalysisFileParser.AdvancedAnalysisParser -c config.json
+```
+
+---
+
+## Configuration
+
+The parser uses config files (JSON) to define how to parse and warn for each file type. Default configs are provided for:
+
+- GBA: `gba_tsv_config.json`
+- SMN: `smn_tsv_config.json`
+- Oncology: `dragen_500_tsv_config.json`
+- JSON: `advConfig.json`
+
+You can override or extend these by providing your own config in the `map_files` key of the request.
+
+### Example request/config structure
+
+| Key           | Type   | Description                                                           |
+| ------------- | ------ | --------------------------------------------------------------------- |
+| `output_json` | string | Filename for the generated JSON (default: `adv_analysis_output.json`) |
+| `input_dir`   | string | Directory containing all input files                                  |
+| `input_files` | list   | (Optional) List of files to parse                                     |
+| `map_files`   | object | (Optional) Mapping of filenames → caller definitions                  |
+
+---
+
+## Warnings
+
+Warnings are generated automatically for each caller/file type, based on the config. Each config defines conditions for warnings (see `*_config.json` files for examples). You can customize these for your use case.
+
+---
+
+## Testing
+
+Run the test suite to validate all parsing and warning logic:
+
+```bash
+pytest AdvancedAnalysisFileParser/Test_AdvancedAnalysisParser.py
+```
+
+Or run the test script:
+
+```bash
+python AdvancedAnalysisFileParser/run_test_parser.py
+```
+
+---
+
+## Example Data
+
+See the `Test/` folder for example input files (TSV/JSON) and expected outputs.
+
+---
+
+## License
+
+MIT

advancedanalysisfileparser-0.1.0.dist-info/RECORD

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advancedanalysisfileparser-0.1.0.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (82.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

advancedanalysisfileparser-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,9 @@
+MIT License
+
+Copyright (c) 2026 Geneyx
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

advancedanalysisfileparser-0.1.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+AdvancedAnalysisFileParser