Data Science for Biologists

Preparing Biologists for the Data Era

Creative Commons License

Python + SQL

Notes

Connecting to the database

import sqlite3 as dbapi
con = dbapi.connect('C:\Users\student\Desktop\portal_mammals.sqlite')
cur = con.cursor()

Querying the database

All records

cur.execute('SELECT mo, dy, yr, plot FROM PortalMammals_main WHERE yr=2002 AND species='SH'')
sh_query = cur.fetchall()
sh_query

One record at a time (because it sometimes it’s lots and lots of records)

cur.execute('SELECT mo, dy, yr, plot FROM PortalMammals_main WHERE yr=2002 AND species='SH'')
record = cur.fetchone()
while record:
    print(record)
    record = cur.fetchone()

Using Python variables inside SQL

cur.execute('SELECT mo, dy, yr, plot FROM PortalMammals_main WHERE yr=? AND species=?', (2001, 'SH'))
sh_query = cur.fetchall()
sh_query

Creating Tables

con = dbapi.connect('C:\Users\student\Desktop\newdatabase.sqlite')
cur = con.cursor()

CREATE TABLE Experiment(
    LoginID TEXT,
    Project TEXT,
    Experiment TEXT,
    Hours REAL,
    ExperimentDate NUM
)

CREATE TABLE Experiments(
    RecordID INTEGER PRIMARY KEY AUTOINCREMENT,
    LoginID TEXT NOT NULL,
    Project TEXT NOT NULL,
    Experiment TEXT NOT NULL,
    Hours REAL,
    ExperimentDate NUM
)

Updating Tables

Adding new records

INSERT INTO Experiment VALUES('epwhite', 'awesomeecology', 1, 18, 2011-11-09)
con.commit()

If not all values are being added

INSERT INTO Experiment (LoginID, Project, Experiment) VALUES('epwhite', 'awesomeecology', 2)
con.commit()

Modifying existing records

UPDATE Experiment SET Hours=10, ExperimentDate=2011-11-08
WHERE LoginID='epwhite' AND Project='awesomeecology' AND Experiment=2
con.commit()

Deleting records

DELETE Experiment
WHERE Project='awesomeecology' AND Experiment=2
con.commit()