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

src/db_utils/__main__.py

@@ -10,8 +10,7 @@ from .config import Config
 from ..logging_conf import logging_def
 from .db_creation import main_create_db
 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
+from .fill_splicing_lore_tables import fill_splicing_lore_data
 import logging
 
 
@@ -24,21 +23,8 @@ def launcher(logging_level: str = "INFO"):
     main_create_db('DISABLE')
     logging.info('Filling cin_gene and cin_exon')
     main_fill_exon_n_gene('DISABLE')
-    # logging.info(f"Creation of {Config.ctrl_exon_file} file")
-    # get_ctrl(Config.exon_intern)
-    # logging.info(f"Creation of {Config.exon_file} file")
-    # get_exon_table(Config.ctrl_exon_file, Config.gene_file, logging_level)
-    # logging.info(f"Creation of {Config.frequency_file} file")
-    # create_freq_table(Config.bed_orf, Config.bed_exon, Config.ctrl_exon_file,
-    #                   logging_level)
-    #
-    # mpopulate = populate.__wrapped__
-    # logging.info(f"Filling {Config.tables[0]} table")
-    # mpopulate(Config.tables[0], Config.gene_file, "y", logging_level)
-    # logging.info(f"Filling {Config.tables[1]} table")
-    # mpopulate(Config.tables[1], Config.exon_file, "y", logging_level)
-    # logging.info(f"Filling {Config.tables[2]} table")
-    # mpopulate(Config.tables[2], Config.frequency_file, "y", logging_level)
+    logging.info('Filling splicing lore tables')
+    fill_splicing_lore_data('DISABLE')
 
 
-launcher(logging_level = "DEBUG")
\ No newline at end of file
+launcher(logging_level="DEBUG")

src/db_utils/config.py

@@ -13,8 +13,11 @@ 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 = ["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'
-
+    data = Path(__file__).parents[2] / 'data'
+    results = Path(__file__).parents[2] / "results"
+    db_file = results / 'chia_pet_database.db'
+    bed_exon = data / 'bed' / 'exon.bed'
+    bed_gene = data / 'bed' / 'gene.bed'
+    ase_event_file = data / 'splicing_lore_data' / 'ase_event.txt'
+    splicing_projects = data / 'splicing_lore_data' / \
+        'splicing_lore_projects.txt'

src/db_utils/fill_splicing_lore_tables.py

+#!/usr/bin/env python3
+
+# -*- coding: UTF-8 -*-
+
+"""
+Description: The goal of this script is to fill the tables \
+cin_ase_event and cin_project_splicing_lore
+"""
+
+from .config import Config
+import pandas as pd
+import logging
+from ..logging_conf import logging_def
+from .populate_database import populate_df
+
+
+def load_splicing_projects() -> pd.DataFrame:
+    """
+    Load the projects of splicing lore database.
+
+    :return: The dataframe of the splicing lore projects
+    """
+    df = pd.read_csv(Config.splicing_projects, sep="\t")
+    logging.debug(df.head())
+    return df
+
+
+def load_ase_event() -> pd.DataFrame:
+    """
+    Load the alternative splicing events of detected in the splicing lore \
+    database.
+
+    :return: The dataframe of splicing lore alternative splicing events
+    """
+    logging.debug('loading cin_project_splicing_lore')
+    df = pd.read_csv(Config.ase_event_file, sep="\t")
+    df.drop(["gene_symbol", "chromosome", "start", "stop", "exons_flanquants"],
+            inplace=True, axis=1)
+    cols = list(df.columns)
+    if cols.index('exon_skipped') != -1:
+        cols[cols.index('exon_skipped')] = 'pos'
+        df.columns = cols
+    df['exon_id'] = df['gene_id'].astype(str) + '_' + df['pos'].astype(str)
+    logging.debug(df.head())
+    return df
+
+
+def fill_splicing_lore_data(logging_level: str = 'DISABLE') -> None:
+    """
+    Fill the tables cin_ase_event and cin_project_splicing_lore
+    """
+    logging_def(Config.results, __file__, logging_level)
+
+    sf_projects = load_splicing_projects()
+    ase_events = load_ase_event()
+    logging.debug('Filling cin_project_splicing_lore')
+    populate_df(table='cin_project_splicing_lore', df=sf_projects, clean='y')
+    logging.debug('Filling cin_ase_event')
+    populate_df(table='cin_ase_event', df=ase_events, clean='y')
+
+
+if __name__ == "__main__":
+    fill_splicing_lore_data('DEBUG')

src/db_utils/populate_database.py

@@ -113,16 +113,31 @@ def insert_data(table: str, content: List[Tuple], cnx: sqlite3.Connection
     cursor.close()
 
 
-def check_table_name(table : str):
+def get_table_names(cnx: sqlite3.Connection) -> List[str]:
+    """
+    Get the list of available table names.
+
+    :param cnx: The connection to ChIA-PET database.
+
+    :return: The list of availbale tables
+    """
+    c = cnx.cursor()
+    c.execute("""SELECT name FROM sqlite_master WHERE type = 'table';""")
+    res = c.fetchall()
+    res = [r[0] for r in res]
+    return res
+
+
+def check_table_name(cnx: sqlite3.Connection, table: str):
     """
     Check if we can use the table name `table`.
 
+    :param cnx: Connection to ChIA-PET database
     :param table: The name of the table to fille
     :return: The same name with the prefix gin if it wasn't here.
     """
-    if "cin" not in table:
-        table = f"cin_{table.lower()}"
-    if table not in Config.tables:
+    tables = get_table_names(cnx)
+    if table not in tables:
         msg = f"The name {table} is not available." \
               f" If the table exist in the database, " \
               f"change the config file to add the table name " \
@@ -175,8 +190,8 @@ def populate_df(table: str, df: pd.DataFrame, clean: str):
     tab.
     :param clean: y to remove the data in the table, n else.
     """
-    table = check_table_name(table)
     cnx = sqlite3.connect(Config.db_file)
+    table = check_table_name(cnx, table)
     check_content_clean_and_insert(table, df, cnx, clean)
 
 
@@ -195,8 +210,8 @@ def populate(table: str, file: str, clean: str, logging_level: str =
     """
     logging_def(Config.db_file.parent, __file__, logging_level)
     mfile = Path(file)
-    table = check_table_name(table)
     cnx = sqlite3.connect(Config.db_file)
+    table = check_table_name(cnx, table)
     check_content_clean_and_insert(table, mfile, cnx, clean)