diff --git a/src/db_utils/__main__.py b/src/db_utils/__main__.py index 35c25348690e699ea6b2373cd5cc34e59cde4dfa..c6679832c5094d22f02a79a4ebed164354dd3346 100755 --- a/src/db_utils/__main__.py +++ b/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 diff --git a/src/db_utils/config.py b/src/db_utils/config.py index 107f80ff26e3623a4dfd3f9c04fbd464d1cadf29..8f9d60ba71004f18633749eb5d45fce0de6e70ff 100755 --- a/src/db_utils/config.py +++ b/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" diff --git a/src/db_utils/creation_of_exon_table.py b/src/db_utils/fill_exon_n_gene_table.py similarity index 100% rename from src/db_utils/creation_of_exon_table.py rename to src/db_utils/fill_exon_n_gene_table.py