Metadata-Version: 2.1
Name: explosig-data
Version: 0.0.1
Summary: Process mutation data into standard formats originally developed for the ExploSig family of tools
Home-page: https://github.com/lrgr/explosig-data
Author: Leiserson Research Group
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: requests (>=2.22.0)
Requires-Dist: pandas (>=0.25.1)
Requires-Dist: numpy (>=1.17.0)
Requires-Dist: snakemake (>=5.3)
Requires-Dist: biopython (>=1.75)
Requires-Dist: twobitreader (>=3.1)
Requires-Dist: tqdm (>=4.39.0)

[![Build Status](https://travis-ci.org/lrgr/explosig-data.svg?branch=master)](https://travis-ci.org/lrgr/explosig-data)
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## ExploSig Data

Helpers for processing mutation data into standard formats originally developed for the [ExploSig](https://github.com/lrgr/explosig) family of tools.

- [Documentation](https://lrgr.github.io/explosig-data/)

### Installation

```sh
pip install explosig-data
```

### Example Usage

```python
>>> import explosig_data as ed

>>> # With chaining
>>> container = (ed
        .standardize_ICGC_ssm_file('path/to/ssm.tsv')
        .extend_df()
        .to_counts_df('SBS_96', ed.categories.SBS_96_category_list())
    )
>>> counts_df = container.counts_dfs['SBS_96']


>>> # Without chaining
>>> ssm_df = ed.standardize_ICGC_ssm_file('path/to/ssm.tsv', wrap=False)
>>> # or
>>> ssm_df = ed.standardize_TCGA_maf_file('path/to/maf.tsv', wrap=False)
>>> extended_df = ed.extend_ssm_df(ssm_df)
>>> counts_df = ed.counts_from_extended_ssm_df(
        extended_df, 
        category_colname='SBS_96', 
        category_values=ed.categories.SBS_96_category_list()
    )
```


### Development

Build and install from the current directory.

```sh
python setup.py sdist bdist_wheel && pip install .
```

