optwps 1.0.0

Fast Window Protection Score calculator for cell-free DNA analysis

optwps

A high-performance Python package for computing Window Protection Score (WPS) from BAM files, designed for cell-free DNA (cfDNA) analysis. It was built as a direct alternative of a script provided by the Kircher Lab, and has been tested to replicate the exact numbers.

Overview

optwps is a fast and efficient tool for calculating Window Protection Scores from aligned sequencing reads. WPS is a metric used in cell-free DNA analysis to identify nucleosome positioning and protected regions by analyzing fragment coverage patterns.

Installation

From Source

pip install optwps

Dependencies

• Python >= 3.7
• pysam
• pandas
• pigz
• tqdm
• bx-python

Usage

Command Line Interface

Basic usage:

optwps -i input.bam -o output.tsv

With custom parameters:

optwps \
    -i input.bam \
    -o output.tsv \
    -w 120 \
    --min_insert_size 120 \
    --max_insert_size 180 \
    --downsample 0.5

Command Line Arguments

• -i, --input: Input BAM file (required)
• -o, --output: Output file path for WPS results. If not provided, results will be printed to stdout. Supports placeholders {chrom} and {target} for creating separate files per chromosome or region (optional)
• -r, --regions: BED file with regions of interest (default: whole genome, optional)
• -w, --protection: Base pair protection window (default: 120)
• --min-insert-size: Minimum read length threshold to consider (optional)
• --max-insert-size: Maximum read length threshold to consider (optional)
• --downsample: Ratio to downsample reads (optional)
• --chunk-size: Chunk size for processing in pieces (default: 1e8)
• --valid-chroms: Comma-separated list of valid chromosomes to include (e.g., '1,2,3,X,Y') or 'canonical' for chromosomes 1-22, X, Y (optional)
• --compute-coverage: If provided, output will include base coverage
• --verbose-output: If provided, output will include separate counts for 'outside' and 'inside' along with WPS

Python API

from optwps import WPS

# Initialize WPS calculator
wps_calculator = WPS(
    protection_size=120,
    min_insert_size=120,
    max_insert_size=180,
    valid_chroms=set(map(str, list(range(1, 23)) + ['X', 'Y']))
)

# Run WPS calculation
wps_calculator.run(
    bamfile='input.bam',
    out_filepath='output.tsv',
    downsample_ratio=0.5
)

Output Format

The output is a tab-separated no-header file with the following columns:

- Chromosome name (without 'chr' prefix)
- Start position (0-based)
- End position (start + 1)
- Base read coverage (if `--compute-coverage`)
- Count of fragments spanning the protection window (if `--verbose-output`)
- Count of fragment endpoints in protection window (if `--verbose-output`)
- Window Protection Score (outside - inside)

Example output:

1\t1000\t1001\t12
1\t1001\t1002\t14
1\t1002\t1003\t10

With --compute-coverage

1\t1000\t1001\t20\t12
1\t1001\t1002\t20\t14
1\t1002\t1003\t19\t10

With --verbose-output:

1\t1000\t1001\t15\t3\t12
1\t1001\t1002\t16\t2\t14
1\t1002\t1003\t14\t4\t10

Algorithm

The Windowed Protection Score algorithm has the following steps:

1. Fragment Collection: For each genomic position, collect all DNA fragments (paired-end reads or single reads) in the region

2. Protection Window: Define a protection window of size protection_size (default 120bp, or ±60bp from the center)

3. Score Calculation:

   • Outside Score: Count fragments that completely span the protection window
   • Inside Score: Count fragment endpoints that fall within the protection window (exclusive boundaries)
   • WPS: Subtract inside score from outside score: WPS = outside - inside

4. Interpretation: Positive WPS values indicate protected regions (likely nucleosome-bound), while negative values suggest accessible regions

Examples

Example 1: Basic WPS Calculation

optwps -i sample.bam -o sample_wps.tsv

Example 2: Providing a regions bed file, limiting the range of the size of the inserts considered, and printing to the terminal

optwps \
    -i sample.bam \
    -r regions.tsv \
    --min_insert_size 120 \
    --max_insert_size 180

Example 3: Specific Regions with Downsampling

optwps \
    -i high_coverage.bam \
    -o wps.tsv \
    --downsample 0.3

Example 4: Creating Separate Output Files per Chromosome

optwps \
    -i sample.bam \
    -o "wps_{chrom}.tsv"

Example 5: Include coverage

optwps \
    -i sample.bam \
    --compute_coverage \
    -o "wps.tsv"