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        "author": "Leiden University Medical Center",
        "author_email": "sasc@lumc.nl",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
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        "description": "# chunked_scatter\n\nThis tool takes a bed file or sequence dictionary as input and divides the\ncontigs/chromosomes into overlapping chunks of a given size. These chunks will\nthen be placed in new bed files, one chromosomes per file. Small chromosomes\nwill be put together to avoid the creation of thousands of files.\n\n## Installation\nInstall from github:\n- Clone the repository: `git clone https://github.com/biowdl/chunked-scatter.git`\n- Enter the repository: `cd chunked-scatter`\n- Install using pip: `pip install .`\n\n## Usage\n```\nchunked-scatter -p output_prefix -i input.bed\n```\nThe input is expected to end in `.bed` or `.dict`!\n\n| option | arguments | definition |\n|-|-|-|\n| -c | a number | The size of the chunks. |\n| -o | a number | The size of the overlap. |\n| -m | a number | The minimum number of bases to be put in a single output file, before a new scatter will be made. |\n\n## Examples\n### bed file\nGiven a bed file located at `/data/regions.bed`:\n```\nchr1\t100\t1000\nchr1\t2000\t16000\nchr2\t5000\t10000\n```\n\nThe command:\n```\nchunked-scatter -p /data/scatter_ -i /data/regions.bed -m 1000 -c 5000\n```\n\nWill produce the following two output files:\n- `/data/scatter_0.bed`:\n  ```\n  chr1\t100\t1000\n  chr1\t2000\t7000\n  chr1\t6850\t12000\n  chr1\t11850\t16000\n  ```\n- `/data/scatter_1.bed`:\n  ```\n  chr2\t5000\t10000\n  ```\n\n### dict file\nGiven a dict file located at `/data/ref.dict`:\n```\n@SQ\tSN:chr1\tLN:3000000\n@SQ SN:chr2 LN:500000\n```\n\nThe command:\n```\nchunked-scatter -p /data/scatter_ -i /data/regions.bed\n```\n\nWill produce the following output file at `/data/scatter_0.bed`:\n```\nchr1\t0\t1000000\nchr1\t999850\t2000000\nchr1\t1999850\t3000000\nchr2\t0\t500000\n```\n\n\n",
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        "keywords": "bioinformatics",
        "license": "MIT",
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        "name": "chunked-scatter",
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        "summary": "Chunk and scatter the regions in a bed or sequence dictfile",
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