Metadata-Version: 2.4
Name: atari
Version: 0.1.0
Summary: AlternaTe Allele Read vIsualizer - A tool for analyzing genomic data from BAM files
Author-email: Samarth Mathur <samarth8392@gmail.com>
License: MIT
Project-URL: Homepage, https://github.com/samarth8392/atari
Project-URL: Bug Tracker, https://github.com/samarth8392/atari/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pandas
Requires-Dist: pysam
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: tqdm
Requires-Dist: rich
Dynamic: license-file

# ATARI - AlternaTe Allele Read vIsualizer

ATARI is a tool for analyzing genomic data from BAM files. It counts reference and alternate alleles at genomic positions and visualizes the results.

## Installation

### From PyPI

```bash
# From PyPI
pip install atari

# From Conda
conda install -c bioconda atari

# Clone the repository
git clone https://github.com/yourusername/atari.git
cd atari

# Option 1: Install with pip
pip install .

# Option 2: Create conda environment from environment.yml
conda env create -f environment.yml
conda activate atari

# usage
# Basic usage with BED file
atari \
  --bam sample1.bam sample2.bam \
  --reference genome.fa \
  --bed regions.bed \
  --window 100 \
  --output results.tsv

# Full pipeline with visualization and gene annotations
atari \
  --bam sample1.bam sample2.bam \
  --reference genome.fa \
  --bed regions.bed \
  --window 100 \
  --output results.tsv \
  --plot \
  --plot-output coverage_plot.png \
  --gtf annotations.gtf \
  --verbose
