From a00438bd9dbf1e15b0613170ccfdfc36fee10f1b Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Tue, 3 Mar 2020 15:04:12 +0100
Subject: [PATCH] src/db_utils/db_creation.py: database creation
---
src/db_utils/db_creation.py | 350 ++++++++++++++++++++++--------------
1 file changed, 212 insertions(+), 138 deletions(-)
diff --git a/src/db_utils/db_creation.py b/src/db_utils/db_creation.py
index d4585149..425441a9 100755
--- a/src/db_utils/db_creation.py
+++ b/src/db_utils/db_creation.py
@@ -3,147 +3,221 @@
# -*- coding: utf-8 -*-
-
-#Creation of the database using Sqlite3 and SQL commands
+"""
+Creation of the database using Sqlite3 and SQL commands
+"""
import sqlite3
-
-
-conn = sqlite3.connect("../../Results/Db_creation/chia_pet_database.db")
-c = conn.cursor()
-
-
-###########################
-# Create table - gin_gene #
-###########################
-c.execute('''CREATE TABLE IF NOT EXISTS gin_gene
- ([name] VARCHAR(30) NOT NULL,
- [id] INT NOT NULL,
- [chromosome] VARCHAR(2) NOT NULL,
- [start] INT NOT NULL,
- [stop] INT NOT NULL,
- [strand] VARCHAR(1) NOT NULL,
- PRIMARY KEY ([id]))''')
-
-
-###########################
-# Create table - gin_exon #
-###########################
-c.execute('''CREATE TABLE IF NOT EXISTS gin_exon
- ([id] VARCHAR(30) NOT NULL,
- [pos] INT NOT NULL,
- [name] VARCHAR(45) NOT NULL,
- [id_gene] INT NOT NULL,
- [chromosome] VARCHAR(2) NOT NULL,
- [start] INT NOT NULL,
- [stop] INT NOT NULL,
- [strand] VARCHAR(1) NOT NULL,
- PRIMARY KEY ([id])
- FOREIGN KEY ([id_gene]) REFERENCES gin_gene([id]))''')
-
-
-##############################
-# Create table - gin_project #
-##############################
-c.execute('''CREATE TABLE IF NOT EXISTS gin_project
- ([id] INT NOT NULL,
- [id_sample] VARCHAR(45) NOT NULL,
- [id_project] VARCHAR(45) NOT NULL,
- [database] VARCHAR(45) NOT NULL,
- [name] VARCHAR(45) NULL,
- [description] TEXT NULL,
- [antiboby] VARCHAR(45) NOT NULL,
- [cell_line] VARCHAR(45) NOT NULL,
- [institute] VARCHAR(45) NULL,
- [citation] VARCHAR(20) NULL,
- PRIMARY KEY ([id]))''')
-
-
-#####################################
-# Create table - gin_gene_frequency #
-#####################################
-c.execute('''CREATE TABLE IF NOT EXISTS gin_gene_frequency
- ([id] INT NOT NULL,
- [ft] VARCHAR(3) NOT NULL,
- [id_gene] INT NOT NULL,
- [frequency] FLOAT NULL,
- PRIMARY KEY ([id]),
- FOREIGN KEY ([id_gene]) REFERENCES gin_gene([id]))''')
-
-
-#####################################
-# Create table - gin_exon_frequency #
-#####################################
-c.execute('''CREATE TABLE IF NOT EXISTS gin_exon_frequency
- ([id] INT NOT NULL,
- [ft] VARCHAR(3) NOT NULL,
- [id_exon] VARCHAR(30) NOT NULL,
- [frequency] FLOAT NULL,
- PRIMARY KEY ([id]),
- FOREIGN KEY ([id_exon]) REFERENCES gin_exon([id]))''')
-
-
-#######################################
-# Create table - gin_exon_interaction #
-#######################################
-c.execute('''CREATE TABLE IF NOT EXISTS gin_exon_interaction
- ([id] INT NOT NULL,
- [force] INT NOT NULL,
- [exon1] VARCHAR(30) NOT NULL,
- [exon2] VARCHAR(30) NOT NULL,
- [id_project] INT NOT NULL,
- [level] VARCHAR(25) NOT NULL,
- PRIMARY KEY ([id]),
- FOREIGN KEY ([exon1]) REFERENCES gin_exon([id]),
- FOREIGN KEY ([exon2]) REFERENCES gin_exon([id]),
- FOREIGN KEY ([id_project]) REFERENCES gin_project([id]))''')
-
-
-#######################################
-# Create table - gin_gene_interaction #
-#######################################
-c.execute('''CREATE TABLE IF NOT EXISTS gin_gene_interaction
- ([id] INT NOT NULL,
- [force] INT NOT NULL,
- [gene1] INT NOT NULL,
- [gene2] INT NOT NULL,
- [id_project] INT NOT NULL,
- [level] VARCHAR(25) NOT NULL,
- PRIMARY KEY ([id]),
- FOREIGN KEY ([gene1]) REFERENCES gin_gene([id]),
- FOREIGN KEY ([gene2]) REFERENCES gin_gene([id]),
- FOREIGN KEY ([id_project]) REFERENCES gin_project([id]))''')
-
-
-############################################
-# Create table - gin_project_splicing_lore #
-############################################
-c.execute('''CREATE TABLE IF NOT EXISTS gin_project_splicing_lore
- ([id] INT NOT NULL,
- [project_name] VARCHAR(45) NULL,
- [source_db] VARCHAR(45) NOT NULL,
- [db_id_project] VARCHAR(15) NOT NULL,
- [sf_name] VARCHAR(45) NOT NULL,
- [cl_name] VARCHAR(45) NOT NULL,
+from .config import Config
+import logging
+from ..logging_conf import logging_def
+
+
+def create_gin_gene_table(conn: sqlite3.Connection) -> None:
+ """
+ Create table gin_gene.
+
+ :param conn: Connection to chia-pet database.
+ """
+ c = conn.cursor()
+ c.execute('''CREATE TABLE IF NOT EXISTS gin_gene
+ ([name] VARCHAR(30) NOT NULL,
+ [id] INT NOT NULL,
+ [chromosome] VARCHAR(2) NOT NULL,
+ [start] INT NOT NULL,
+ [stop] INT NOT NULL,
+ [strand] VARCHAR(1) NOT NULL,
PRIMARY KEY ([id]))''')
-
-
-############################
-# Create table - ase_event #
-############################
-c.execute('''CREATE TABLE IF NOT EXISTS ase_event
+ conn.commit()
+
+
+def create_gin_exon_table(conn: sqlite3.Connection) -> None:
+ """
+ Create table gin_exon.
+
+ :param conn: Connection to chia-pet database.
+ """
+ c = conn.cursor()
+ c.execute('''CREATE TABLE IF NOT EXISTS gin_exon
+ ([id] VARCHAR(30) NOT NULL,
+ [pos] INT NOT NULL,
+ [name] VARCHAR(45) NOT NULL,
+ [id_gene] INT NOT NULL,
+ [chromosome] VARCHAR(2) NOT NULL,
+ [start] INT NOT NULL,
+ [stop] INT NOT NULL,
+ [strand] VARCHAR(1) NOT NULL,
+ PRIMARY KEY ([id])
+ FOREIGN KEY ([id_gene]) REFERENCES gin_gene([id]))''')
+ conn.commit()
+
+
+def create_gin_projects_table(conn: sqlite3.Connection) -> None:
+ """
+ Create table gin_project.
+
+ :param conn: Connection to chia-pet database.
+ """
+ c = conn.cursor()
+ c.execute('''CREATE TABLE IF NOT EXISTS gin_projects
+ ([id] INT NOT NULL,
+ [id_sample] VARCHAR(45) NOT NULL,
+ [id_project] VARCHAR(45) NOT NULL,
+ [database] VARCHAR(45) NOT NULL,
+ [name] VARCHAR(45) NULL,
+ [description] TEXT NULL,
+ [antiboby] VARCHAR(45) NOT NULL,
+ [cell_line] VARCHAR(45) NOT NULL,
+ [institute] VARCHAR(45) NULL,
+ [citation] VARCHAR(20) NULL,
+ PRIMARY KEY ([id]))''')
+ conn.commit()
+
+
+def create_gin_gene_frequency_table(conn: sqlite3.Connection) -> None:
+ """
+ Create table gin_gene_frequency.
+
+ :param conn: Connection to chia-pet database.
+ """
+ c = conn.cursor()
+ c.execute('''CREATE TABLE IF NOT EXISTS gin_gene_frequency
+ ([id] INT NOT NULL,
+ [ft] VARCHAR(3) NOT NULL,
+ [id_gene] INT NOT NULL,
+ [frequency] FLOAT NULL,
+ PRIMARY KEY ([id]),
+ FOREIGN KEY ([id_gene]) REFERENCES gin_gene([id]))''')
+ conn.commit()
+
+
+def create_gin_exon_frequency_table(conn: sqlite3.Connection) -> None:
+ """
+ Create table gin_exon_frequency.
+
+ :param conn: Connection to chia-pet database.
+ """
+ c = conn.cursor()
+ c.execute('''CREATE TABLE IF NOT EXISTS gin_exon_frequency
([id] INT NOT NULL,
- [id_project] INT NOT NULL,
- [gene_id] INT NOT NULL,
- [pos] INT NOT NULL,
- [exon_id] VARCHAR(30) NOT NULL,
- [delta_psi] FLOAT NULL,
- [pvalue] FLOAT NULL,
- [pvalue_glm_cor] FLOAT NULL,
+ [ft] VARCHAR(3) NOT NULL,
+ [id_exon] VARCHAR(30) NOT NULL,
+ [frequency] FLOAT NULL,
PRIMARY KEY ([id]),
- FOREIGN KEY ([exon_id]) REFERENCES gin_exon([id]),
- FOREIGN KEY ([gene_id]) REFERENCES gin_gene([id]),
- FOREIGN KEY ([id_project]) REFERENCES gin_project_splicing_lore([id]))''')
-
-conn.commit()
\ No newline at end of file
+ FOREIGN KEY ([id_exon]) REFERENCES gin_exon([id]))''')
+ conn.commit()
+
+
+def create_gin_exon_interaction_table(conn: sqlite3.Connection) -> None:
+ """
+ Create table gin_exon_interaction.
+
+ :param conn: Connection to chia-pet database.
+ """
+ c = conn.cursor()
+ c.execute('''CREATE TABLE IF NOT EXISTS gin_exon_interaction
+ ([id] INT NOT NULL,
+ [force] INT NOT NULL,
+ [exon1] VARCHAR(30) NOT NULL,
+ [exon2] VARCHAR(30) NOT NULL,
+ [id_project] INT NOT NULL,
+ [level] VARCHAR(25) NOT NULL,
+ PRIMARY KEY ([id]),
+ FOREIGN KEY ([exon1]) REFERENCES gin_exon([id]),
+ FOREIGN KEY ([exon2]) REFERENCES gin_exon([id]),
+ FOREIGN KEY ([id_project]) REFERENCES gin_project([id]))''')
+ conn.commit()
+
+
+def create_gin_gene_interaction_table(conn: sqlite3.Connection) -> None:
+ """
+ Create table gin_gene_interaction.
+
+ :param conn: Connection to chia-pet database.
+ """
+ c = conn.cursor()
+ c.execute('''CREATE TABLE IF NOT EXISTS gin_gene_interaction
+ ([id] INT NOT NULL,
+ [force] INT NOT NULL,
+ [gene1] INT NOT NULL,
+ [gene2] INT NOT NULL,
+ [id_project] INT NOT NULL,
+ [level] VARCHAR(25) NOT NULL,
+ PRIMARY KEY ([id]),
+ FOREIGN KEY ([gene1]) REFERENCES gin_gene([id]),
+ FOREIGN KEY ([gene2]) REFERENCES gin_gene([id]),
+ FOREIGN KEY ([id_project]) REFERENCES gin_project([id]))''')
+ conn.commit()
+
+
+def create_gin_project_splicing_lore_table(conn: sqlite3.Connection) -> None:
+ """
+ Create table gin_project_splicing_lore
+
+ :param conn: Connection to chia-pet database.
+ """
+ c = conn.cursor()
+ c.execute('''CREATE TABLE IF NOT EXISTS gin_project_splicing_lore
+ ([id] INT NOT NULL,
+ [project_name] VARCHAR(45) NULL,
+ [source_db] VARCHAR(45) NOT NULL,
+ [db_id_project] VARCHAR(15) NOT NULL,
+ [sf_name] VARCHAR(45) NOT NULL,
+ [cl_name] VARCHAR(45) NOT NULL,
+ PRIMARY KEY ([id]))''')
+ conn.commit()
+
+
+def create_gin_ase_event_table(conn: sqlite3.Connection) -> None:
+ """
+ Create table ase_event.
+
+ :param conn: Connection to chia-pet database.
+ """
+ c = conn.cursor()
+ c.execute('''CREATE TABLE IF NOT EXISTS gin_ase_event
+ ([id] INT NOT NULL,
+ [id_project] INT NOT NULL,
+ [gene_id] INT NOT NULL,
+ [pos] INT NOT NULL,
+ [exon_id] VARCHAR(30) NOT NULL,
+ [delta_psi] FLOAT NULL,
+ [pvalue] FLOAT NULL,
+ [pvalue_glm_cor] FLOAT NULL,
+ PRIMARY KEY ([id]),
+ FOREIGN KEY ([exon_id]) REFERENCES gin_exon([id]),
+ FOREIGN KEY ([gene_id]) REFERENCES gin_gene([id]),
+ FOREIGN KEY ([id_project])
+ REFERENCES gin_project_splicing_lore([id]))''')
+ conn.commit()
+
+
+def main_create_db(logging_level: str = "DISABLE"):
+ """
+ Create an empty chia-pet database.
+ """
+ logging_def(Config.db_file.parent, __file__, logging_level)
+ conn = sqlite3.connect(Config.db_file)
+ logging.debug('Creation of gin_gene')
+ create_gin_gene_table(conn)
+ logging.debug('Creation of gin_exon')
+ create_gin_exon_table(conn)
+ logging.debug('Creation of gin_project_gene')
+ create_gin_projects_table(conn)
+ logging.debug('Creation of gin_gene_frequency_table')
+ create_gin_gene_frequency_table(conn)
+ logging.debug('Creation of gin_exon_frequency_table')
+ create_gin_exon_frequency_table(conn)
+ logging.debug('Creation of gin_exon_interaction_table')
+ create_gin_exon_interaction_table(conn)
+ logging.debug('Creation of gin_gene_interaction_table')
+ create_gin_gene_interaction_table(conn)
+ logging.debug('Creation of gin_project_splicing_lore_table')
+ create_gin_project_splicing_lore_table(conn)
+ logging.debug('Creation of gin_ase_event_table')
+ create_gin_ase_event_table(conn)
+
+
+if __name__ == "__main__":
+ main_create_db("DEBUG")
--
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