From c5f457760b0445b55bd2a1972ea1da373e4d837f Mon Sep 17 00:00:00 2001
From: alapendr <audrey.lapendry@ens-lyon.fr>
Date: Fri, 10 Apr 2020 09:40:20 +0200
Subject: [PATCH] __main__.py: update to integrate the filling of
cin_exon_interaction and cin_gene_interaction tables
---
src/db_utils/__main__.py | 22 ++++++++++++++++++++++
1 file changed, 22 insertions(+)
diff --git a/src/db_utils/__main__.py b/src/db_utils/__main__.py
index 355ec694..5b7637e9 100755
--- a/src/db_utils/__main__.py
+++ b/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")
--
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