update

src/find_interaction_cluster/community_file_tools/community_file_2_gene_list.py

@@ -14,6 +14,7 @@ from typing import Dict, List
 
 import lazyparser as lp
 import pandas as pd
+import polars as pl
 
 from ...figures_utils.config_figures import Config as ConfF
 from ..config import Config
@@ -73,7 +74,6 @@ def create_df_4_a_community(
     community: str,
     size: int,
     dic_id: Dict[int, str],
-    hg38_dic: Dict[int, str],
 ) -> pd.DataFrame:
     """
     Create a small dataframe based on a string containing gene id separated \
@@ -84,8 +84,6 @@ def create_df_4_a_community(
     belongs
     :param size: The size a the community
     :param dic_id: A dicitonary linking id of gene to their symbol
-    :param hg38_dic: A dicitonary linking id of gene to their hg38 symbol
-    :return: A dataframe containing
 
     >>> create_df_4_a_community('1, 2, 3', 'C4', 3, {1: 'DSC2', 2: 'DSC1', 3:
     ... 'DSG1', 4: 'DSG4', 5: 'KCTD4', 6: 'TPT1'}, {1: 'DSC2-38', 2: 'DSC1', 3:
@@ -97,18 +95,15 @@ def create_df_4_a_community(
     """
     gene_ids = get_gene_list(gene_str)
     gene_names = [dic_id[gn] for gn in gene_ids]
-    gene_names_hg38 = [hg38_dic.get(gn, "") for gn in gene_ids]
     if len(gene_names) != size:
         raise ValueError(
-            f"gene name size ({len(gene_names)})"
-            f" and size ({size}) differt! "
+            f"gene name size ({len(gene_names)}) and size ({size}) differt! "
         )
     return pd.DataFrame(
         {
             "cluster": [community] * size,
             "size": [size] * size,
-            "fasterdb_symbol": gene_names,
-            "hg38_symbol": gene_names_hg38,
+            "symbol": gene_names,
             "gene_id": gene_ids,
         }
     )
@@ -132,10 +127,9 @@ def create_full_df(df: pd.DataFrame) -> pd.DataFrame:
     4      C2     2           KCTD4       KCTD4        5
     """
     dic_id = create_gene_dic()
-    hg38_dic = create_hg38_dic()
     df_list = [
         create_df_4_a_community(
-            row["genes"], row["community"], row["nodes"], dic_id, hg38_dic
+            row["genes"], row["community"], row["nodes"], dic_id
         )
         for _, row in df.iterrows()
     ]
@@ -156,7 +150,16 @@ def gene_table_creator(community_file: str, outname: str = "") -> None:
     df = load_community_file(Path(community_file))
     df = create_full_df(df)
     outf = outname or Path(community_file).stem
-    df.to_csv(output / f"{outf}.csv", sep="\t", index=False)
+    df = pl.from_pandas(df)
+    df = df.with_columns(
+        symbol=pl.col("symbol")
+        .over("cluster", mapping_strategy="join")
+        .list.join(", "),
+        gene_id=pl.col("gene_id")
+        .over("cluster", mapping_strategy="join")
+        .list.join(", "),
+    ).unique()
+    df.write_csv(output / f"{outf}.csv", separator="\t")
 
 
 if __name__ == "__main__":