gc_stats.py

#!/usr/bin/env python3

# -*- coding: UTF-8 -*-

"""
Description: The goal of this script is make a statistical analysis
"""

import pandas as pd
from typing import List, Any
from scipy.stats import mannwhitneyu
from itertools import combinations


def mann_whitney(df: pd.DataFrame) -> List[Any]:
    """
    Return the man withney test comparing the gc content and the different \
    regions in the dataframe.

    :param df: A dataframe of gc content
    :return: The name of the groups and their p-value
    """
    regions = df['region'].unique()
    for r1, r2 in combinations(regions, 2):
        v1 = df.loc[df['region'] == r1, "gc_content"]
        v2 = df.loc[df['region'] == r2, "gc_content"]
        return [r1, r2, mannwhitneyu(v1, v2)[-1]]


def make_stat(df: pd.DataFrame) -> List[List[Any]]:
    """

    :param df: A dataframe of gc content
    :return: The list of pvalues of interest
    """
    if len(df['location'].unique()) == 1:
        return [mann_whitney(df)]
    else:
        list_pval = []
        for loc in df['location'].unique():
            df_tmp = df.loc[df["location"] == loc, :]
            res = mann_whitney(df_tmp)
            res[0] = (loc, res[0])
            res[1] = (loc, res[1])
            list_pval.append(res)
        return list_pval