COSMIC database bug fixed

Author: mishugeb

.DS_Store

@@ -0,0 +1,2 @@
+include sigproSS/input/*
+include sigproSS/input/vcf/*

LICENSE

@@ -9,86 +9,47 @@ $pip install sigproSS
 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')
+>> 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_ 
+### importdata 
 
 
     Imports the path of example data.
 
-    importdata(inpute_type="vcf")
+    importdata()
 
-    Example 1: 
-    ----------
-    To import an example vcf project provided with the package:
-    
-    >>> from sigproSS import spss 
-    >>> data = spss.importdata("vcf")
-    
-    This "data" variable can be used as a parameter of the first argument of the single_sample function.
-        
-    
-    Example 2: 
-    ----------
-    To import an example csv96 file (for more description please the singple_sample_pcwag function) provided with the           package:
-        
-    >>> from sigproSS import spss 
-    >>> data = spss.importdata("pcwag96")
-    
-    This "data" variable can be used as a parameter of the first argument of the single_sample_pcwag function.
-    
-    Example 3: 
-    ----------
-    To import an example csv192 file (for more description please the singple_sample_pcwag function) provided with the           package:
-        
+    Example: 
+    -------
     >>> from sigproSS import spss 
-    >>> data = spss.importdata("pcwag192")
+    >>> data = spss.importdata()
+    This "data" variable can be used as a parameter of the first argument of the sigproSS function.
 
-    This "data" variable can be used as a parameter of the second argument of the single_sample_pcwag function.
+    To get help on the parameters and outputs of the "importdata" function, please write down the following line:
 
-   **To get more description on the parameters and outputs of the "importdata" function, please write down the following line:**
+    >>> help(spss.importdata)
 
-     >>> help(spss.importdata)
-    
-### _single_sample_
+### single_sample
 
     Decompose the query samples into the global signatures.
 
-    single_sample(data, output, ref="GRCh37", sig_database = "default", check_rules = True, exome=False)
+    single_sample(vcf, outputdir, exome=False)
 
     Example: 
     -------
     >>> from sigproSS import spss 
-    >>> data = spss.importdata() ##'you can put the path of your own vcf project here'
+    >>> data = spss.importdata()
     >>> spss.single_sample(data, "results", ref="GRCh37", exome=False)
 
-   **To get more description on the parameters and outputs of the "single_sample" function, please write down the following line:**
+    To get help on the parameters and outputs of the "importdata" function, please write down the following line:
 
     >>> help(spss.single_sample)
-    
-### _single_sample_pcwag_
-    Decompose the query samples those are in pcwag format into the global signatures.
-    
-    single_sample_pcwag(csv96, csv192="", output="results", par_one=0.01, par_two=0.025, n_cpu=-1)
-    
-    Example: 
-    -------
-    >>> from sigproSS import spss, spss_pcwag 
-    >>> csv96 = spss.importdata("pcwag96")  #'you can put the path of your own csv96 file here'
-    >>> csv192 = spss.importdata("pcwag192") #''you can put the path of your own csv192 file here'
-    >>> spss_pcwag.single_sample_pcwag(csv96, csv192, output="example_output")
-    
-  **To get more description on the parameters and outputs of the "single_sample_pcwag" function, please write down the following line:**
-    
-    >>> help(spss_pcwag.single_sample_pcwag)   
-    
 ## 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.