src/find_interaction_cluster/clip_figures/clip_analyser.py : changes in...

src/find_interaction_cluster/clip_figures/clip_analyser.py : changes in create_figure and in clip_folder_analysis to be able to create figures of exons regulated by a splicing factor

src/find_interaction_cluster/clip_figures/clip_analyser.py

@@ -406,7 +406,7 @@ def add_regulation_column(df_table: pd.DataFrame, sf_name: str, feature: str,
 
 def create_figure(project: str, weight: int, global_weight: int,
                   same_gene: bool, inflation: float, cell_line: str,
-                  feature: str, clip_file: Path,
+                  feature: str, clip_file: Union[Path, Tuple],
                   feature_bed: Path, test_type: str = "permutation",
                   iteration: int = 10000, display_size: bool = False,
                   community_file: str = "", sl_reg: bool = False) -> None:
@@ -443,20 +443,26 @@ def create_figure(project: str, weight: int, global_weight: int,
                                              same_gene, inflation, cell_line,
                                              feature, community_file)
     output.mkdir(exist_ok=True, parents=True)
-    outfile = output / f"{clip_file.name.split('.')[0]}.pdf"
+    my_name = clip_file.name.split('.')[0] if isinstance(clip_file, Path) \
+        else "_".join(clip_file)
+    outfile = output / f"{my_name}.pdf"
     final_table = create_table(feature, clip_file, feature_bed, com_file)
+    my_name = clip_file.name.split("_")[0] if isinstance(clip_file, Path) \
+        else "_".join(clip_file)
     if sl_reg:
         final_table = add_regulation_column(final_table,
-                                            clip_file.name.split("_")[0],
+                                            my_name,
                                             feature)
     my_col = "peak_density" \
         if "peak_density" in final_table.columns else "regulation"
+    print(outfile)
     create_community_fig(final_table, feature, my_col, outfile,
                          test_type, iteration=iteration,
                          display_size=display_size)
 
 
-def clip_folder_analysis(clip_folder: Path, project: str, weight: int,
+def clip_folder_analysis(clip_folder: Union[Path, Tuple], project: str,
+                         weight: int,
                          global_weight: int, same_gene: bool, inflation: float,
                          cell_line: str,
                          feature: str, test_type: str = "permutation",
@@ -494,8 +500,11 @@ def clip_folder_analysis(clip_folder: Path, project: str, weight: int,
     logging_def(ConfigGraph.community_folder, __file__, logging_level)
     feature_bed = ConfigClip.bed_gene if feature == "gene" \
         else ConfigClip.bed_exon
-    files = list(clip_folder.glob("*.bed")) + \
-        list(clip_folder.glob("*.bed.gz"))
+    if isinstance(clip_folder, Path):
+        files = list(clip_folder.glob("*.bed")) + \
+            list(clip_folder.glob("*.bed.gz"))
+    else:
+        files = [clip_folder]
     pool = mp.Pool(processes=min(len(files), ps))
     processes = []
     for mfile in files: