Installation and Usage of the bamnado Package

Installation

To install the bamnado package, follow these steps:

1. Install Rust: Ensure you have Rust installed on your system. You can install it using rustup:

   curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
   

2. Clone the Repository: Clone the bamnado repository to your local machine:

   git clone https://github.com/your-repo/bamnado.git
   cd bamnado
   

3. Install: Ensure you have Python and maturin installed:

   pip install maturin
   

   Then, build and install the Python package:

   pip install .
   

Usage

The bamnado package provides a command-line interface (CLI) for processing BAM files. Below is an example of its usage.

Example: Filtering Reads from a BAM File

Command

The following command filters reads from a BAM file based on specific criteria and writes the coverage to a bedGraph file:

bamnado bam-coverage \
  --bam input.bam \
  --output output.bedgraph \
  --bin-size 100 \
  --norm-method rpkm \
  --scale-factor 1.5 \
  --use-fragment \
  --proper-pair \
  --min-mapq 30 \
  --min-length 50 \
  --max-length 500 \
  --blacklisted-locations blacklist.bed \
  --whitelisted-barcodes barcodes.txt

Explanation of Options

• --bam: Path to the input BAM file.
• --output: Path to the output file (e.g., bedGraph or BigWig).
• --bin-size: Size of genomic bins for coverage calculation.
• --norm-method: Normalization method (raw, rpkm, or cpm).
• --scale-factor: Scaling factor for normalization.
• --use-fragment: Use fragments instead of individual reads for counting.
• --proper-pair: Include only properly paired reads.
• --min-mapq: Minimum mapping quality for reads to be included.
• --min-length: Minimum read length.
• --max-length: Maximum read length.
• --blacklisted-locations: Path to a BED file specifying regions to exclude.
• --whitelisted-barcodes: Path to a file with barcodes to include.

Output

The output file (output.bedgraph) will contain the normalized coverage data for the BAM file, filtered based on the specified criteria.

Additional Commands

Multi-BAM Coverage

To calculate coverage from multiple BAM files:

bamnado multi-bam-coverage \
  --bams file1.bam file2.bam \
  --output output.bedgraph \
  --bin-size 100 \
  --norm-method rpkm \
  --scale-factor 1.5 \
  --use-fragment \
  --proper-pair \
  --min-mapq 30 \
  --min-length 50 \
  --max-length 500

Split BAM File into Endogenous and Exogenous Reads

To split a BAM file into endogenous and exogenous reads:

bamnado split-exogenous \
  --input input.bam \
  --output output_prefix \
  --exogenous-prefix "exo_" \
  --stats stats.json \
  --allow-unknown-mapq \
  --proper-pair \
  --min-mapq 30 \
  --min-length 50 \
  --max-length 500

Split BAM File by Cell Barcodes

To split a BAM file based on cell barcodes:

bamnado split \
  --input input.bam \
  --output output_prefix \
  --whitelisted-barcodes barcodes.txt \
  --proper-pair \
  --min-mapq 30 \
  --min-length 50 \
  --max-length 500

Help

For more details on available commands and options, run:

bamnado --help