src/find_interaction_cluster/clip_figures/clip_analyser.py: fix bedtools intersect function

src/find_interaction_cluster/clip_figures/clip_analyser.py

@@ -50,7 +50,7 @@ def bedtools_intersect(gene_bed: Path, clip_bed: Path,
 
     """
     res = sp.check_output(f"bedtools intersect -a {gene_bed} "
-                          f"-b {clip_bed} -c", shell=True)
+                          f"-b {clip_bed} -c -s", shell=True)
     res = StringIO(str(res, "utf-8"))
     id_col = f"id_{feature}"
     columns = ["chr", "start", "end", id_col, "name", "strand", "clip_peak"]
@@ -182,7 +182,7 @@ def create_table(feature: str, clip_file: Path,
     :param com_file: A file containing communities
     :return: The final dataframe that can be used to create clip figures
 
-    >>> cf = find_or_create_community("", 3, 3, True, 1.5, "gene")
+    >>> cf = find_or_create_community("", 3, 3, True, 1.5, "ALL", "gene")
     >>> create_table("gene", ConfigClip.test_clip_bed,
     ... ConfigClip.test_gene_bed, cf)
         id_gene  clip_peak  peak_density community  community_size
@@ -407,6 +407,7 @@ def clip_folder_analysis(clip_folder: Path, project: str, weight: int,
         processes.append(pool.apply_async(create_figure, args))
     [p.get(timeout=None) for p in processes]
 
+
 if __name__ == "__main__":
     import doctest
     doctest.testmod()
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