Metadata-Version: 2.1
Name: chunked-scatter
Version: 0.1.0
Summary: Chunk and scatter the regions in a bed or sequence dictfile
Home-page: https://github.com/biowdl/chunked-scatter
Author: Leiden University Medical Center
Author-email: sasc@lumc.nl
License: MIT
Description: # 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
        ```
        
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Description-Content-Type: text/markdown
