Merge branch 'master' of gitbio.ens-lyon.fr:LBMC/regards/chia-pet_network

src/db_utils/__main__.py

@@ -9,7 +9,7 @@ Description: Populate the gin database
 from .config import Config
 from ..logging_conf import logging_def
 from .db_creation import main_create_db
-from .creation_of_exon_table import main_fill_exon_n_gene
+from .fill_exon_n_gene_table import main_fill_exon_n_gene
 # from .create_freq_table import create_freq_table
 # from .populate_database import populate
 import logging

src/db_utils/config.py

@@ -7,9 +7,6 @@ Description: Configuration class
 """
 
 from pathlib import Path
-from typing import Dict, Any
-import logging
-import logging.config
 
 
 class Config:
@@ -20,12 +17,4 @@ class Config:
     tables = ["cin_gene", "cin_exon", "cin_frequency", "cin_interaction"]
     bed_exon = Path(__file__).parents[2] / 'data' / 'bed' / 'exon.bed'
     bed_gene = Path(__file__).parents[2] / 'data' / 'bed' / 'gene.bed'
-    # bed_orf = Path(__file__).parents[1] / "data" / "exon_orf.bed"
-    # bed_exon_freq = Path(__file__).parents[1] / "data" / "exon_freq.bed"
-    # output = Path(__file__).parents[2] / "results"
-    # exon_intern = Path(__file__).parents[1] / "data" / "exon_intern.bed"
-    # ctrl_exon_file = output / "CTRL_exons.txt"
-    # exon_file = output / "exons.txt"
-    # gene_file = Path(__file__).parents[1] / "data" / "genes.csv"
-    # frequency_file = output / "frequency.txt"