sigproextractor 0.0.5.39

Extracts mutational signatures from mutational catalogues

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