chunked-scatter 0.1.0

Chunk and scatter the regions in a bed or sequence dictfile

chunked_scatter

This tool takes a bed file or sequence dictionary as input and divides the contigs/chromosomes into overlapping chunks of a given size. These chunks will then be placed in new bed files, one chromosomes per file. Small chromosomes will be put together to avoid the creation of thousands of files.

Installation

Install from github:

• Clone the repository: git clone https://github.com/biowdl/chunked-scatter.git
• Enter the repository: cd chunked-scatter
• Install using pip: pip install .

Usage

chunked-scatter -p output_prefix -i input.bed

The input is expected to end in .bed or .dict!

option	arguments	definition
-c	a number	The size of the chunks.
-o	a number	The size of the overlap.
-m	a number	The minimum number of bases to be put in a single output file, before a new scatter will be made.

Examples

bed file

Given a bed file located at /data/regions.bed:

chr1	100	1000
chr1	2000	16000
chr2	5000	10000

The command:

chunked-scatter -p /data/scatter_ -i /data/regions.bed -m 1000 -c 5000

Will produce the following two output files:

• /data/scatter_0.bed:

  chr1	100	1000
  chr1	2000	7000
  chr1	6850	12000
  chr1	11850	16000
  

• /data/scatter_1.bed:

  chr2	5000	10000
  

dict file

Given a dict file located at /data/ref.dict:

@SQ	SN:chr1	LN:3000000
@SQ SN:chr2 LN:500000

The command:

chunked-scatter -p /data/scatter_ -i /data/regions.bed

Will produce the following output file at /data/scatter_0.bed:

chr1	0	1000000
chr1	999850	2000000
chr1	1999850	3000000
chr2	0	500000