atari 0.1.1

AlternaTe Allele Read vIsualizer - A tool for analyzing genomic data from BAM files

🎮 Atari

AlternaTe Allele Read vIsualizer

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Atari is a command-line tool to count reference and alternate alleles from BAM files across genomic regions and visualize allele depths.
It uses pysam for BAM parsing, matplotlib for plotting, and supports flexible input with BED files or manual region specification.

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✨ Features

• Count reference and alternate reads per position
• Aggregate counts into non-overlapping windows
• Apply quality filters (mapping, base quality, depth)
• Output clean TSV tables
• Generate high-quality plots
• Annotate visualizations with genes from GTF files
• Multi-sample comparisons
• Detailed per-base alternate allele breakdown (A, C, G, T, DEL, INS, N)

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📦 Installation

git clone https://github.com/yourusername/atari.git
cd atari
pip install -r requirements.txt

Requirements:

• Python ≥ 3.7
• pysam
• matplotlib
• numpy
• pandas
• tqdm
• rich

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🚀 Quick Start

Ensure BAM and FASTA files are indexed (.bai, .fai).

1. Basic Usage

python atari.py \
  --bam sample1.bam sample2.bam \
  --reference genome.fa \
  --bed regions.bed \
  --window 100 \
  --output results.tsv

2. Full Pipeline with Visualization and Gene Annotation

python atari.py \
  --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

3. Analyze Specific Chromosomal Region

python atari.py \
  --bam sample.bam \
  --reference genome.fa \
  --chromosome chr20 \
  --start 1000000 \
  --end 1100000 \
  --window 100 \
  --output chr20_results.tsv \
  --plot \
  --plot-output chr20_coverage.png

4. Detailed Base-Level Counts

python atari.py \
  --bam sample.bam \
  --reference genome.fa \
  --bed regions.bed \
  --window 100 \
  --output detailed_results.tsv \
  --detailed \
  --verbose

Argument	Description	Required
--bam	BAM file(s) (indexed)	✅
--reference	Reference FASTA (indexed)	✅
--bed	BED file with regions	➡️ (or --chromosome)
--chromosome	Chromosome name (e.g., chr1)	➡️ (or --bed)
--start, --end	Region coordinates (if using --chromosome)	✅
--window	Window size in bp for summarization	✅
--output	Output file name (TSV)	✅
--plot	Generate plot	Optional
--plot-output	Plot output file	Optional
--gtf	Gene annotations (GTF format)	Optional
--verbose	Verbose mode	Optional
...and many more! (see --help)

🐛 Troubleshooting

1. Ensure your BAM and FASTA files are indexed (.bai and .fai present).
2. Use --verbose to print detailed processing steps.
3. For debugging errors, set ATARI_DEBUG=1 environment variable.

👨‍💻 Contributing

PRs welcome! Feel free to open issues for bugs, feature requests, or improvements.

📫 Contact

For questions, contact [e-mail].