begin work towards processing stats for compat testing

scripts/ref_genome_validating/stats_compat_testing.py

@@ -0,0 +1,56 @@
+# This script is for creating graphs for the ref_genome compat testing
+# PEP : donaldcampbelljr/refgenome_compat_testing:default
+import copy
+import os
+import numpy as np
+import requests
+import pephubclient
+import pandas as pd
+import seaborn as sns
+import matplotlib.pyplot as plt
+import matplotlib.colors as mcolors
+from scipy.cluster.hierarchy import linkage
+
+try:
+    PEP_URL = os.environ["PEP_URL"]
+except:
+    # pep url
+    PEP_URL = "donaldcampbelljr/refgenome_compat_testing:default"
+
+
+def main():
+
+    # pull from tier rating column to get the final assessment
+    tier_rating_keys = ["mm10", "hg38", "hg19"]
+
+    # reported_ref_genome column should have one of these values
+    human_keys = [
+        " GRCh38",
+        " hg38",
+        " hg19",
+        " GRCh38/hg38",
+        " grch38",
+        " grch38/hg38",
+    ]
+    mouse_keys = [" mm10"]
+
+    results_path = os.path.abspath("stats_results")
+    project = pephubclient.PEPHubClient()
+    peppyproject = project.load_project(project_registry_path=PEP_URL)
+    df = copy.deepcopy(peppyproject.sample_table)
+
+    df["reported_ref_genome"] = df["reported_ref_genome"].replace(
+        {" GRCh38": "human"}, inplace=True
+    )
+
+    # Standardize the human data
+    # for human_designator in human_keys:
+    #     df['reported_ref_genome'] = df['reported_ref_genome'].replace({" GRCh38": 'human'})
+    # df['reported_ref_genome'] = df['reported_ref_genome'].apply(lambda x: 'human' if x in human_keys else x)
+    # df['reported_ref_genome'] = df['reported_ref_genome'].str.lower().replace({human_designator: 'human'})
+
+    print(df["reported_ref_genome"].head())
+
+
+if __name__ == "__main__":
+    main()