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        "author": "S Mishu Ashiqul Islam",
        "author_email": "m0islam@ucsd.edu",
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        "description": "# SigProfilerExtractor\nSigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. \nThe tool identifies the number of operative mutational signatures, their activities in each sample, and the probability \nfor each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator \nand SigProfilerPlotting. \n\n## INSTALLATION\nIn the commandline, please type the following line:\n```\n$pip install sigproextractor\n```\nInstall your desired reference genome from the command line/terminal as follows (available reference genomes are: GRCh37, GRCh38, mm9, and mm10):\n```\n$ python\n>> from SigProfilerMatrixGenerator import install as genInstall\n>> genInstall.install('GRCh37')\n```\nThis will install the human 37 assembly as a reference genome. You may install as many genomes as you wish.\n\nopen a python interpreter and import the SigProfilerExtractor module. Please see the examples of the functions. \n\n## FUNCTIONS\n\n### importdata \n\n\n    Imports the path of example data.\n\n    importdata(datatype=\"matobj\")\n\n    Example: \n    -------\n    >>> from sigproextractor import sigpro as sig\n    >>> data = sig.importdata(\"text\")\n    This \"data\" variable can be used as a parameter of the \"project\" argument of the sigProfilerExtractor function.\n\n    To get help on the parameters and outputs of the \"importdata\" function, please write down the following line:\n\n    >>> help(sig.importdata)\n\n\n### sigProfilerExtractor \n\n\n    Extracts mutational signatures from an array of samples.\n\n    sigProfilerExtractor(input_type, out_put, project, refgen=\"GRCh37\", startProcess=1, endProcess=10, totalIterations=8, \n    cpu=-1, hierarchy = False, mtype = [\"default\"],exome = False, indel_extended = False)\n\n\n\n    Examples\n    --------\n\n    >>> from sigproextractor import sigpro as sig\n    >>> data = sig.importdata(\"vcf\")\n    >>> sig.sigProfilerExtractor(\"vcf\", \"example_output\", data, startProcess=1, endProcess=3)\n\n    Wait untill the excecution is finished. The process may a couple of hours based on the size of the data.\n    Check the current working directory for the \"example_output\" folder.\n\n    To get help on the parameters and outputs of the \"sigProfilerExtractor\" function, please write down the following line:\n\n    >>> help(sig.sigProfilerExtractor)\n\n\n## COPYRIGHT\nThis software and its documentation are copyright 2018 as a part of the sigProfiler project. The SigProfilerExtractor framework is free software and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.\n\n## CONTACT INFORMATION\nPlease address any queries or bug reports to S M Ashiqul Islam (Mishu) at m0islam.ucsd.edu\n\n\n",
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        "license": "UCSD",
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        "name": "new-sigproextractor",
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        "summary": "Extracts mutational signatures from mutational catalogues",
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