__main__.py: update to integrate the filling of cin_exon_interaction and...

__main__.py: update to integrate the filling of cin_exon_interaction and cin_gene_interaction tables

src/db_utils/__main__.py

@@ -15,6 +15,24 @@ from .frequency_scripts.create_n_fill_exon_frequency_file import \
     fill_frequency_tables
 import logging
 from .projects_metadata.get_fill_metadata import fill_projects_table
+import subprocess
+
+
+def launch_features_interactions(opt: str):
+    """
+    Allows to launch the script features_interactions.py:
+    - to determine which couples of genomic regions interact, e.g. exons or
+    genes, that for each ChIA-PET dataset
+    - to fill the cin_gene_interaction and cin_exon_interaction tables
+
+    :param opt: which genomic regions are we studying, --exon or --gene
+    """
+    subprocess.check_call(f"for file in `ls {Config.chia_pet_files}" f"/*` ; "
+                          f"do " f"basename_file=$(basename -s .bed " f"$file)"
+                          f" ; " f"python -m "
+                          f"src.db_utils.interactions.features_interactions " 
+                          "${basename_file} " f"{opt} ; done", shell=True,
+                          stderr=subprocess.STDOUT)
 
 
 def launcher(logging_level: str = "INFO"):
@@ -32,6 +50,10 @@ def launcher(logging_level: str = "INFO"):
     fill_frequency_tables(Config.cpu, 'DISABLE')
     logging.info('Filling projects table')
     fill_projects_table('DISABLE')
+    logging.info('Filling cin_exon_interaction table')
+    launch_features_interactions("--exon")
+    logging.info('Filling cin_gene_interaction table')
+    launch_features_interactions("--gene")
 
 
 launcher(logging_level="DEBUG")