vmwhere 0.2.0__tar.gz

vmwhere-0.2.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          pip install -e ".[dev]"
+
+      - name: Run tests
+        run: pytest tests/ -v --tb=short

vmwhere-0.2.0/.github/workflows/release.yml

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+name: Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+permissions:
+  contents: write
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install build dependencies
+        run: pip install build setuptools-scm>=8
+
+      - name: Build package
+        run: python -m build
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-pypi:
+    needs: build
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Create GitHub Release
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          gh release create "${{ github.ref_name }}" dist/* \
+            --title "${{ github.ref_name }}" \
+            --generate-notes

vmwhere-0.2.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# PyPI configuration file
+.pypirc
+
+# Auto-generated version file (setuptools-scm)
+src/vmwhere/_version.py
+
+# Claude Code
+CLAUDE.md

vmwhere-0.2.0/LICENSE

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vmwhere-0.2.0/PKG-INFO

@@ -0,0 +1,166 @@
+Metadata-Version: 2.4
+Name: vmwhere
+Version: 0.2.0
+Summary: Genotyping and sequence-resolved allele calling for tandem repeat regions
+Author-email: Sara Peterson <skpet@unc.edu>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/pirl-unc/vmwhere
+Project-URL: Bug Tracker, https://github.com/pirl-unc/vmwhere
+Keywords: genotyping,tandem repeats,sequence decomposition,ewing sarcoma,microsatellite
+Requires-Python: >=3.12.4
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas>=2.2.0
+Requires-Dist: pysam>=0.22.1
+Requires-Dist: biopython>=1.84
+Requires-Dist: python-Levenshtein>=0.27.1
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.1.0; extra == "dev"
+Dynamic: license-file
+
+<div align="center">
+  <img src="vmwhere_sky_logo.png" alt="logo" width="400"/>
+</div>
+
+# variant motif where? variant motif here!
+
+vmwhere (VariantMotifwhere) is a tool for analyzing tandem repeat (microsatellite) regions from long-read sequencing data. It provides three core capabilities:
+
+1. **Discovery** — identify microsatellite coordinates in a reference genome
+2. **Genotyping** — call allele length, repeath length, and motif-level sequence decomposition at each locus
+3. **Visualization** — generate sequence-resolved allele frequency plots
+
+---
+
+## Installation
+
+VMwhere is available as a Python package:
+
+```bash
+pip install vmwhere
+```
+
+---
+## Requirements
+
+- **Python** >= 3.12.4
+
+- **R** (>= 4.0) — required only for the `visualize` subcommand.
+  Install required R packages:
+
+  ```bash
+  Rscript -e "install.packages(readLines('requirements-r.txt'), repos='https://cloud.r-project.org')"
+  ```
+
+---
+
+## Usage
+
+### 1. Find microsatellites
+
+Scan a reference FASTA for tandem repeat regions matching a given motif.
+
+```bash
+vmwhere find \
+  --motif GGAA \
+  --perfect_repeats 4 \
+  --max_gap 50 \
+  --buffer_size 50 \
+  --fasta data/reference.fasta \
+  --output_dir output/
+```
+
+This outputs a BED file (`microsatellite_coordinates.bed`) with columns: `chr`, `start`, `end`, `region_id`, `motif`.
+
+#### Parameters
+| Flag | Description |
+|------|-------------|
+| `--motif` / `-m` | Repeat motif sequence to search for (e.g., `GGAA`) |
+| `--fasta` / `-f` | Path to the reference genome FASTA |
+| `--output_dir` / `-o` | Output directory |
+| `--perfect_repeats` / `-r` | Minimum number of uninterrupted tandem repeats to call a microsatellite (default: 2) |
+| `--max_gap` / `-g` | Maximum base pairs between adjacent microsatellites before they are treated as distinct loci (default: 50) |
+| `--buffer_size` / `-b` | Base pairs to extend beyond the outermost repeat on each side (default: 50) |
+
+See [`examples/run_vmwhere_find.sh`](examples/run_vmwhere_find.sh) for a runnable example.
+
+### 2. Genotype microsatellites
+
+Extract reads overlapping each locus, decompose sequences into motif and non-motif segments, cluster reads by Levenshtein distance, and call alleles.
+
+```bash
+vmwhere genotype \
+  --sample_id example_sample \
+  --bed_file data/T2T_regions.bed \
+  --bam_file data/A673_sampled_reads.sorted.bam \
+  --fasta data/GCF_009914755.1_T2T-CHM13v2.0_chr6_chr10.fasta \
+  --cluster_distance 4 \
+  --minor_threshold 0.20 \
+  --major_threshold 0.80 \
+  --output_dir output/ \
+  --num_processes 2
+```
+
+See [`examples/run_vmwhere_genotype.sh`](examples/run_vmwhere_genotype.sh) for a runnable example.
+
+#### Parameters
+
+**Required:**
+
+| Flag | Description |
+|------|-------------|
+| `--sample_id` | Sample identifier (used in output filename) |
+| `--bam_file` | Path to sorted, indexed BAM file |
+| `--fasta` | Path to the reference genome FASTA |
+| `--bed_file` | Headerless BED file with columns: `chr`, `start`, `end`, `region_id`, `motif` |
+| `--output_dir` | Output directory (file will be named `<sample_id>_vmwhere_results.tsv`) |
+
+**Optional:**
+
+| Flag | Description | Default |
+|------|-------------|---------|
+| `--cluster_distance` | Maximum Levenshtein distance for grouping reads into a cluster | 0 |
+| `--minor_threshold` | Minimum read support fraction to call a minor allele | 0.20 |
+| `--major_threshold` | Minimum read support fraction to call a homozygous genotype | 0.80 |
+| `--num_processes` | Number of parallel processes | 24 |
+
+
+#### Output TSV columns
+
+The output follows VCF-style conventions but is written as a TSV for simpler parsing.
+
+| Column | Description |
+|--------|-------------|
+| `CHROM` | Chromosome |
+| `POS` | Start coordinate of the microsatellite |
+| `ID` | Locus identifier from the input BED file |
+| `REF` | Reference allele sequence |
+| `ALT` | Alternate allele sequence(s); `.` if none |
+| `END` | End coordinate of the microsatellite |
+| `MOTIF` | Canonical repeat motif |
+| `GT` | Genotype (e.g., `0/0` = homozygous reference, `0/1` = heterozygous) |
+| `AL` | Allele length in base pairs |
+| `CN` | Total copy number of the canonical motif (consecutive and interrupted occurrences) |
+| `CNM` | Maximum uninterrupted copy number of the canonical motif (e.g., `6GGAA_1GGAT_2GGAA` = 6) |
+| `MD` | Motif purity — fraction of allele base pairs matching the canonical motif |
+| `DS_READ` | Decomposed sequence of the allele |
+| `DS_REF` | Decomposed sequence of the reference |
+| `RS` | Read support for the allele |
+
+
+### 3. Visualize alleles at a microsatellite
+
+Generate a PDF showing sequence-resolved allele structures and their frequencies at a given locus.
+
+```bash
+vmwhere visualize \
+  --genotype_tsv output/example_sample_vmwhere_results.tsv \
+  --microsatellite_id chr6_region_41 \
+  --min_allele_count 0 \
+  --output_pdf output/chr6_region_41_visualization.pdf
+```
+
+See [`examples/run_vmwhere_visualize.sh`](examples/run_vmwhere_visualize.sh) for a runnable example.
+
+