src/bed_handler/__main__.py: add a parameter include0 to include exons...

src/bed_handler/__main__.py: add a parameter include0 to include exons containing CTCF if wanted. Add a parameter near_ctcf that allows to recover regulated exons far from a CTCF site

src/bed_handler/__main__.py

@@ -17,16 +17,18 @@ def launcher():
     """
     Create the necessary bed file to visualise bigwig file
     """
-    write_regulated_gene_file()
-    create_filtered_bed()
-    create_region_bed()
-    create_bed_ctcf_exon("down", 0, "both")
-    create_bed_ctcf_exon("down", 1000, "both")
-    create_bed_ctcf_exon("down", 2000, "both")
-    create_bed_ctcf_exon("down", 1000, "upstream")
-    create_bed_ctcf_exon("down", 2000, "upstream")
-    create_bed_ctcf_exon("down", 1000, "downstream")
-    create_bed_ctcf_exon("down", 2000, "downstream")
+    # write_regulated_gene_file()
+    # create_filtered_bed()
+    # create_region_bed()
+    create_bed_ctcf_exon("down", 0, "both", True)
+    create_bed_ctcf_exon("down", 1000, "both", False)
+    create_bed_ctcf_exon("down", 2000, "both", False)
+    create_bed_ctcf_exon("down", 2000, "both", True)
+    create_bed_ctcf_exon("down", 2000, "both", True, False)
+    create_bed_ctcf_exon("down", 1000, "upstream", False)
+    create_bed_ctcf_exon("down", 2000, "upstream", False)
+    create_bed_ctcf_exon("down", 1000, "downstream", False)
+    create_bed_ctcf_exon("down", 2000, "downstream", False)
 
 
 launcher()