src/db_utils/config.py: modification of prefixes gin to cin in Config.table +...

src/db_utils/config.py: modification of prefixes gin to cin in Config.table + creation of Config.bed_exon and Config.bed_gene variable

src/db_utils/config.py

@@ -17,13 +17,15 @@ class Config:
     A class containing every parameters used in the submodule db_utils
     """
     db_file = Path(__file__).parents[2] / "results" / 'chia_pet_database.db'
-    tables = ["gin_gene", "gin_exon", "gin_frequency", "gin_interaction"]
-    bed_orf = Path(__file__).parents[1] / "data" / "exon_orf.bed"
-    bed_exon = 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"
+    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"