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
3 maintainers
Metadata
3 maintainers
Release files for sigproSS 0.0.0.27
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| sigproSS-0.0.0.27.tar.gz | 4.7 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| sigproSS-0.0.0.27-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 9.6 MB
Release files / sigproSS-0.0.0.27.tar.gz
| Download URL | sigproSS-0.0.0.27.tar.gz |
|---|---|
| Size | 4.7 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
66e267ca2ed4b9cdb1bb80bb7b5bec2748eb800344a0e53e812ef68da4fed8c6
|
|
BLAKE2b-256 checksum How to use checksums |
c982fbd3b010c1e2ab403c426833ab239307f91a32ff9a3be5c09abd41e1afc1
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.2.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/47.3.1.post20200622 requests-toolbelt/0.9.1 tqdm/4.47.0 CPython/3.7.6
|
Release files / sigproSS-0.0.0.27-py3-none-any.whl
| Download URL | sigproSS-0.0.0.27-py3-none-any.whl |
|---|---|
| Size | 4.9 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
1d6cf8255849c7d5587aa5199c7db5a56f93c0cf396d70a5c21a9e165ecc7ec4
|
|
BLAKE2b-256 checksum How to use checksums |
5091c69a1f4a082e698e03cd3b544afeecfb505dca9c43ea1e5e47fad094011e
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.2.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/47.3.1.post20200622 requests-toolbelt/0.9.1 tqdm/4.47.0 CPython/3.7.6
|
