Metadata-Version: 2.1
Name: sigproSS
Version: 0.0.0.25
Summary: Decomposes mutational catalogues to mutational signatures
Home-page: https://github.com/AlexandrovLab/SigProfilerExtractor.git
Author: S Mishu Ashiqul Islam
Author-email: m0islam@ucsd.edu
License: UCSD
Platform: UNKNOWN
Description-Content-Type: text/markdown
Requires-Dist: matplotlib (>=2.2.2)
Requires-Dist: scipy (>=1.1.0)
Requires-Dist: numpy (>=1.14.4)
Requires-Dist: pandas (>=0.23.4)
Requires-Dist: SigProfilerMatrixGenerator (>=0.1.20)
Requires-Dist: sigProfilerPlotting (>=0.1.17)
Requires-Dist: sigproextractor (>=0.0.5.6)
Requires-Dist: statsmodels (>=0.9.0)
Requires-Dist: scikit-learn (>=0.20.2)
Requires-Dist: lxml (>=4.3.0)

# SigProfilerSingleSample
SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability for each signature to cause a specific mutation type in the sample. The tool makes use of SigProfilerMatrixGenerator, SigProfilerExtractor and SigProfilerPlotting. 

## INSTALLATION
In the commandline, please type the following line:
```
$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')
```
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()

    Example: 
    -------
    >>> from sigproSS import spss 
    >>> data = spss.importdata()
    This "data" variable can be used as a parameter of the first argument of the sigproSS function.

    To get help on the parameters and outputs of the "importdata" function, please write down the following line:

    >>> help(spss.importdata)

### single_sample

    Decompose the query samples into the global signatures.

    single_sample(vcf, outputdir, exome=False)

    Example: 
    -------
    >>> from sigproSS import spss 
    >>> data = spss.importdata()
    >>> spss.single_sample(data, "results", ref="GRCh37", exome=False)

    To get help on the parameters and outputs of the "importdata" function, please write down the following line:

    >>> help(spss.single_sample)
## 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


