.. Copyright (C) 2023 Roberto Rossini SPDX-License-Identifier: MIT Reading interactions #################### ``hictk`` supports reading interactions from .hic and .cool files using the ``hictk dump`` command. By default, interactions are dumped to stdout in COO format (row, column, count): .. code-block:: console user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1kbp 7 7 1745 7 12 1766 7 17 1078 ... Use the option ``--join`` to instead dump interactions in bedgraph2 format: .. code-block:: console user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.mcool --resolution 1kbp --join | head -n 3 chr2L 7000 8000 chr2L 7000 8000 1745 chr2L 7000 8000 chr2L 12000 13000 1766 chr2L 7000 8000 chr2L 17000 18000 1078 All operations work on .hic as well as .[m]cool files: .. code-block:: console user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.mcool --resolution 1kbp | head -n 3 7 7 1745 7 12 1766 7 17 1078 user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.mcool::/resolutions/1000 | head -n 3 7 7 1745 7 12 1766 7 17 1078 Dump balanced or expected interactions: .. code-block:: console user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1kbp --join --balance SCALE | head -n 3 chr2L 7000 8000 chr2L 7000 8000 1681.679565429688 chr2L 7000 8000 chr2L 12000 13000 1386.554565429688 chr2L 7000 8000 chr2L 17000 18000 878.9703979492188 user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1kbp --join --matrix-type expected | head -n 3 chr2L 7000 8000 chr2L 7000 8000 88.33206176757812 chr2L 7000 8000 chr2L 12000 13000 63.43805313110352 chr2L 7000 8000 chr2L 17000 18000 31.78345680236816 Dump interactions overlapping a region of interest: .. code-block:: console user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1kbp --join --range chr3L:20,000,000-25,000,000 | head -n 3 chr3L 20002000 20003000 chr3L 20002000 20003000 2390 chr3L 20002000 20003000 chr3L 20007000 20008000 1285 chr3L 20002000 20003000 chr3L 20012000 20013000 490 user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1kbp --join --range chr3L:20,000,000-25,000,000 --range2 chrX | head -n 3 chr3L 20002000 20003000 chrX 52000 53000 1 chr3L 20002000 20003000 chrX 157000 158000 1 chr3L 20002000 20003000 chrX 352000 353000 1 Dump tables other than pixels: .. code-block:: console user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --table chroms | head -n 3 chr2L 23513712 chr2R 25286936 chr3L 28110227 user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --table normalizations SCALE VC VC_SQRT user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --table resolutions | head -n 3 1000 5000 10000 See hictk dump help message for the complete list of supported tables. Dump cis or trans interactions only: .. code-block:: console user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1kbp --cis-only --join | head -n 3 chr2L 7000 8000 chr2L 7000 8000 1745 chr2L 7000 8000 chr2L 12000 13000 1766 chr2L 7000 8000 chr2L 17000 18000 1078 user@dev:/tmp$ hictk dump data/4DNFIZ1ZVXC8.hic9 --resolution 1kbp --trans-only --join | head -n 3 chr2L 7000 8000 chr2R 27000 28000 1 chr2L 7000 8000 chr2R 322000 323000 1 chr2L 7000 8000 chr2R 397000 398000 1