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        "description": ".. |bs| replace:: **bgsignature**\n\nBGSignature\n===========\n\n|bs| is a package used to compute signatures.\n\nThe most basic type of computation is the computation\nof the counts of the different k-mers (e.g. 3 or 5).\nThis computation can be done for a set of mutations,\nfor a set of regions or for a set of mutation\nthat fall within certain regions.\n\n\n|bs| consists of 3 tools:\n\n- **count**: count different k-mers\n- **frequency**: divide the counts by the total counts\n- **normalize**: divide the counts by counts obtained\n  separately and normalize the results.\n\n**Advanced features** include:\n\n- ability to group the counts (e.g. group mutations by sample)\n- normalize the counts by the context taken from a regions file\n- collapse (add together) reverse complementary sequences\n\n\n\nInstallation\n------------\n\nThis project is a Python package\nand can be installed with ``pip``.\nDownload the source code, get into this\nproject directory and execute:\n\n.. code:: bash\n\n   pip install .\n\n\nUsage\n-----\n\nCommand line interface\n**********************\n\nThe 3 tools can be called using\n\n- *bgsignature count*\n- *bgsignature frequency*\n- *bgsignature normalize*\n\nSome examples:\n\n- getting help:\n\n    .. code:: bash\n\n       bgsignature -h\n       bgsignature frequency -h\n\n- count triplets in mutation that fall in certain regions using hg38:\n\n    .. code:: bash\n\n       bgsignature count -m my/muts/file -r my/regions/file\n       -g hg38 -o my/output.json --cores 4\n\n\nPython\n******\n\nAlternative, the command line options have an equivalent in Python:\n\n.. code:: python\n\n   from bgsignature import count, relative_frequency, normalize\n\nthat accept similar parameters except the output.\nThe return object can be used as a dictionary.\n\nIf you already have your files loaded in Python\nyou can use directly count function\nin the corresponding module.\nE.g.:\n\n.. code:: python\n\n   from bgsignature.count import mutation\n   mutation.count(mutations, 'hg38', 3)\n\nIn addition, you can also\nuse the the \"low-level\" functions that\ndo the count (``count_all``\nand ``count_group``)\nwhich are much simple and do not\nperform any kind of parallelization.\nE.g.:\n\n.. code:: python\n\n   from bgsignature.count import mutation\n   mutation.count_all(mutations, 'hg38', 3)\n   # or to group mutations by sample\n   mutation.count_group(mutations, 'hg38', 3, 'SAMPLE')\n\n\nThe return object can be normalized to 1,\nusing the ``sum1()`` method\nor divided by some normalization counts\nusing the ``normalize()`` method.\n\n\n\nImportant\n---------\n\nThere are some behavioural characteristics that\nmust be taken into account:\n\n- |bs| filters out mutations whose reference nucleotide\n  (as provided in the file), and the\n  corresponding one in the reference genome do not match.\n\n- when using the ``collapse`` option (enabled by default),\n  |bs| does not remove one of the collapsed sequences but keeps both.\n  This means that you need to manually remove the ones you\n  are not interested in.\n\n- when using ``bgsignature.count.mutation.count``\n  or ``bgsignature.count.region.count`` function\n  and a number of ``cores`` for paralelization,\n  the ``chunk`` parameter must be selected\n  adequately, as a it can have a huge impact on performance.\n\nFile formats\n------------\n\nMutations file\n**************\n\nTab separated file\n(can be compressed into ``gz``, ``bgz`` or ``xz`` formats)\nwith a header and at least these columns:\n``CHROMOSOME``, ``POSITION``, ``REF``, ``ALT``.\nIn addition, ``SAMPLE``, ``CANCER_TYPE`` and ``SIGNATURE``\nare optional columns that can be used for\ngrouping the signature.\n\n\nRegions file\n************\n\nTab separated file\n(can be compressed into ``gz``, ``bgz`` or ``xz`` formats)\nwith a header and at least these columns:\n``CHROMOSOME``, ``START``, ``END``, ``ELEMENT``.\nIn addition, ``SYMBOL``, and ``SEGMENT``\nare optional columns that can be used for\ngrouping the signature.\n\n\n\nSupport\n-------\n\nIf you are having issues, please let us know.\nYou can contact us at: bbglab@irbbarcelona.org",
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        "license": "Apache Software License 2.0",
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