explosig-data 0.0.1

Process mutation data into standard formats originally developed for the ExploSig family of tools

ExploSig Data

Helpers for processing mutation data into standard formats originally developed for the ExploSig family of tools.

• Documentation

Installation

pip install explosig-data

Example Usage

>>> 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.

python setup.py sdist bdist_wheel && pip install .