unduliner 1.0.0__tar.gz

unduliner-1.0.0/DESCRIPTION.md

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+Unduliner is a Python command-line tool for predicting whether genomic variants are associated with 
+local DNA methylation changes using nanopore long-read sequencing data.
+
+It integrates MM/ML-tagged BAM files, VCFs, and a pre-trained deep learning model to evaluate methylation 
+differences around SNVs and structural variants.
+
+Usage details and test data are available on the [Github page](https://github.com/Chisomgold/unduliner/tree/main)

unduliner-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Halimat Chisom Atanda
+
+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.

unduliner-1.0.0/MANIFEST.in

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+recursive-include unduliner/model *.pth
+include *.md

unduliner-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: unduliner
+Version: 1.0.0
+Summary: CLI tool to link variants to methylation changes from nanopore data
+Author-email: Halimat Chisom Atanda <gearthdexter@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2025 Halimat Chisom Atanda
+        
+        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.
+        
+Project-URL: Source, https://github.com/Chisomgold/unduliner
+Project-URL: Documentation, https://github.com/Chisomgold/unduliner/tree/main#unduliner
+Keywords: genomics,bioinformatics,dna-methylation,variant-calling
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch
+Requires-Dist: torch-summary
+Requires-Dist: torchvision
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: pysam
+Requires-Dist: bx-python
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: numpy
+Requires-Dist: pillow
+Dynamic: license-file
+
+Unduliner is a Python command-line tool for predicting whether genomic variants are associated with 
+local DNA methylation changes using nanopore long-read sequencing data.
+
+It integrates MM/ML-tagged BAM files, VCFs, and a pre-trained deep learning model to evaluate methylation 
+differences around SNVs and structural variants.
+
+Usage details and test data are available on the [Github page](https://github.com/Chisomgold/unduliner/tree/main)

unduliner-1.0.0/README.md

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+# **unduliner**
+
+### *Predicting methylation-altering single nucleotide variants (SNVs) and structural variants (SVs) from nanopore sequencing*
+
+`unduliner` is a Python package designed to predict whether a somatic variant is associated with local methylation change, 
+using nanopore long-read sequencing and a pre-trained deep learning model.
+
+The tool takes as input:
+
+* One BAM file (Nanopore reads with MM/ML tags)
+* One VCF file
+* A trained model (`.pth`, included in the `model/` directory and added by default to options)
+
+It extracts genomic regions around each variants, evaluates methylation differences using a statistical and deep learning pipeline, 
+and predicts whether the variant is likely to cause a methylation shift.
+
+---
+
+## **Features**
+
+* Predicts SNV- and SV-associated methylation alterations
+* Works directly on Nanopore MM/ML–tagged BAMs
+* User-configurable methylation thresholds
+* Outputs an interpretable table including DMRs and methylation deltas
+* Supports GTF and regulatory elements annotation of identified regions
+
+---
+
+## **Installation**
+
+`pip install unduliner`
+
+### **Alternatively, clone the repository**
+
+```bash
+git clone https://github.com/Chisomgold/unduliner.git
+cd unduliner
+```
+
+### **Create environment**
+
+```bash
+conda env create -f unduliner.yml
+conda activate unduliner
+pip install -e $PWD
+unduliner -h
+```
+
+
+
+---
+
+## **Usage**
+
+### **Required arguments**
+
+| Argument  | Description                                              |
+| --------- | -------------------------------------------------------- |
+| `--bam`   | Nanopore BAM file with MM/ML tags                        |
+| `--vcf`   | VCF file containing SNVs                                 |
+
+### **Some optional arguments**
+
+| Argument          | Default                | Description                                                     |
+| ----------------- | ---------------------- | --------------------------------------------------------------  | 
+| `--chromosome`    | -                      | Chromosome of interest (e.g., chr10)                            |
+| `--region`        | -                      | Region of interest (e.g. chr10:3000-4000)                       |
+| `--mincov`        | 3                      | Minimum read coverage per allele                                |
+| `--mincpgs`       | 3                      | Minimum CpGs required within region                             |
+| `--cpgdist`       | 50                     | Maximum distance allowed between consecutive CpGs               |
+| `--meth_cutoff`   | 0.8                    | Probability threshold for calling methylated                    |
+| `--unmeth_cutoff` | 0.2                    | Probability threshold for calling unmethylated                  |
+| `--tmp`           | working dir            | Dir that supports read/write of many files                      |
+| `--gtf`           | -                      | Tabix-indexed GTF file to annotated diff methylated regions     |
+| `--cre`           | -                      | CRE file for annotation                                         |
+| `--sv`            | -                      | Activates functions for SVs - INS,DEL,BND,DUP,INV               |
+---
+
+## **Example command**
+
+```bash
+unduliner -b testdata/chr17_2M_225M.bam -v testdata/chr17atcc.vcf.gz 
+
+#optionally add --gtf path/to/sorted.gtf.gz --cre path/to/promoters.bed --cre path/to/repeatsWG.bed
+```
+
+### for SV
+```bash
+unduliner -b sample.bam -v SV.vcf.gz --model model/pretrained80.pth --sv
+```
+
+
+---
+
+# **Output**
+
+`unduliner` generates a tab-delimited table summarising methylation effects per variant.
+
+### **Minimal Output Table**
+
+| Chr   | Start     | End       | Ref | Alt | Reads_with_Ref | Reads_with_Alt | Prediction | Top 5 DMHs                  | Meth-prop-diffs  |
+| ----  | --------- | --------- | --- | --- | -------------  | -------------- | ---------- | --------------------------- | ---------------- |
+| chr17 | 21552714  | 21552715  | C   | T   | 26             | 6              | Positive   | 21551211-21551853=2.854e-56 | 0.642            |
+| chr17 | 20194148  | 20194149  | A   | G   | 8              | 25             | Negative   | 20174773-20174843=5.040e-02 | 0.376            |  
+| chr17 | 21276148  | 21276149  | C   | A   | 8              | 12             | Amb        | 21275234-21276360=2.852e-04 | 0.180            |
+
+
+
+### Column descriptions
+
+* **Prediction:** “Positive” = variant likely associated with nearby methylation change, "Amb" = unsure (e.g., insufficient reads)
+* **Top 5 DMHs:** <= 5 Genomic intervals with smallest adjusted p-values
+* **Meth-prop-diffs:** Δ(methylation) between ref-allele reads and alt-allele reads, where a negative value means reduced 
+methylation on the variant reads compared to the reference.
+* **Start/End:** The SNV genomic coordinate (End = variant position)
+* Extra columns for GTF and CREs by user-request. The `--cre` option can be used multiple times; files should be tab/space-delimited.
+Only the first 4 columns will be used with chr, start, end, as the first 3 columns respectively and the fourth column is a 
+genomic feature relevant to that region like promoter, enhancer, repeats, etc. 
+
+---
+
+
+## **Citing unduliner**
+
+If you use **unduliner** in your research, please cite the repository:
+
+
+A manuscript is in preparation.
+
+---
+
+## **License**
+
+MIT License

unduliner-1.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "unduliner"
+version = "1.0.0"
+description = "CLI tool to link variants to methylation changes from nanopore data"
+readme = "DESCRIPTION.md"
+license = { file = "LICENSE" }
+authors = [
+    { name = "Halimat Chisom Atanda", email = "gearthdexter@gmail.com" }
+]
+requires-python = ">=3.10"
+
+dependencies = [
+    "torch",
+    "torch-summary",
+    "torchvision",
+    "matplotlib",
+    "seaborn",
+    "pysam",
+    "bx-python",
+    "scikit-learn",
+    "scipy",
+    "numpy",
+    "pillow"
+]
+
+keywords = ["genomics", "bioinformatics", "dna-methylation", "variant-calling"]
+
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Operating System :: OS Independent",
+]
+
+[project.scripts]
+unduliner = "unduliner.cli:main"
+
+[tool.setuptools]
+packages = ["unduliner", "unduliner.model"]
+
+[project.urls]
+Source = "https://github.com/Chisomgold/unduliner"
+Documentation = "https://github.com/Chisomgold/unduliner/tree/main#unduliner"

unduliner-1.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

unduliner-1.0.0/setup.py

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+#!/usr/bin/env python
+
+from setuptools import setup, find_packages
+
+setup()

unduliner-1.0.0/unduliner/__init__.py

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+