Metadata-Version: 2.1
Name: sigproextractor
Version: 0.0.5.47
Summary: Extracts mutational signatures from mutational catalogues
Home-page: https://github.com/AlexandrovLab/SigProfilerExtractor.git
Author: S Mishu Ashiqul Islam
Author-email: m0islam@ucsd.edu
License: UCSD
Description: # SigProfilerExtractor
        SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. 
        The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability 
        for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator 
        and SigProfilerPlotting. 
        
        ## INSTALLATION
        In the commandline, please type the following line:
        ```
        $pip install sigproextractor
        ```
        Install your desired reference genome from the command line/terminal as follows (available reference genomes are: GRCh37, GRCh38, mm9, and mm10):
        ```
        $ python
        >> from SigProfilerMatrixGenerator import install as genInstall
        >> genInstall.install('GRCh37')
        ```
        This will install the human 37 assembly as a reference genome. You may install as many genomes as you wish.
        
        open a python interpreter and import the SigProfilerExtractor module. Please see the examples of the functions. 
        
        ## FUNCTIONS
        
        ### importdata 
            
            
            Imports the path of example data.
            
            importdata(datatype="matobj")
        
            Example: 
            -------
            >>> from sigproextractor import sigpro as sig
            >>> data = sig.importdata("text")
            This "data" variable can be used as a parameter of the "project" argument of the sigProfilerExtractor function.
            
            To get help on the parameters and outputs of the "importdata" function, please write down the following line:
            
            >>> help(sig.importdata)
                
        
        ### sigProfilerExtractor 
            
            
            Extracts mutational signatures from an array of samples.
            
            sigProfilerExtractor(input_type, out_put, project, refgen="GRCh37", startProcess=1, endProcess=10, totalIterations=8, 
            cpu=-1, hierarchy = False, mtype = ["default"],exome = False, indel_extended = False)
            
            
            
            Examples
            --------
            
            >>> from sigproextractor import sigpro as sig
            >>> data = sig.importdata("vcf")
            >>> sig.sigProfilerExtractor("vcf", "example_output", data, startProcess=1, endProcess=3)
            
            Wait untill the excecution is finished. The process may a couple of hours based on the size of the data.
            Check the current working directory for the "example_output" folder.
            
            To get help on the parameters and outputs of the "sigProfilerExtractor" function, please write down the following line:
            
            >>> help(sig.sigProfilerExtractor)
            
            
        ## COPYRIGHT
        This 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.
        
        ## CONTACT INFORMATION
        Please address any queries or bug reports to S M Ashiqul Islam (Mishu) at m0islam.ucsd.edu
        
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