gtars-fragsplit

Split fragment files according to pseudobulk assignments for single-cell ATAC-seq data processing.

Features

• Efficient fragment file splitting
• Pseudobulk generation from single-cell data
• Support for cell type annotations
• Gzip compression support
• Memory-efficient streaming

Usage

Command Line

gtars fragsplit \
  --fragments fragments.tsv.gz \
  --barcodes barcodes.txt \
  --output-dir pseudobulk/

From Python

from gtars import fragsplit

fragsplit.split_by_clusters(
    fragments="fragments.tsv.gz",
    clusters="clusters.csv",
    output_dir="pseudobulk/"
)

Input Formats

Fragment File

Standard 10x Genomics format:

chr1    1000    1500    AAACCCAAGAAACACT-1    1

Barcode Assignment

AAACCCAAGAAACACT-1    cluster1
AAACCCAAGAAACAGC-1    cluster2

Output

Creates one fragment file per cluster/pseudobulk group with appropriate cell barcodes.