1. Class #2: Introduction to MySQL (Continued) Where clause (continued) Aggregate Functions Creating users Backing up your database Indexes (if time) Importing large datasets (if time) Make sure you receive Class notes Exercise handout

2. Where Clause How do you think we can limit the results from the last query to just gene “TNFRSF18”? Remember the query is: SELECT gene.name, organism.species FROM gene, organism WHERE gene.organism_id=organism.organism_id;

3. Where Clause (Continued) SELECT gene.name, organism.species FROM gene, organism WHERE gene.organism_id=organism.organism_id AND gene.name=‘TNFRSF18’;

4. Aggregate Functions What if we want to know how many genes we have? SELECT count(gene_id) FROM gene; What if we want to count the number of records for each gene name? SELECT name, COUNT(gene_id) FROM gene GROUP BY name;

6. What if we want to know how many genes (by name) have more than one record in our gene table? SELECT name, COUNT(gene_id) AS copies FROM gene GROUP BY name HAVING copies>1; Here we restricted the results based on properties of the group. Having Clause

7. Backing Up your Database From the command line (not in MySQL): mysqldump -uusername -p databasename > filename.sql Example: mysqldump -uroot trii > triibackup.sql (our database has no password) filename.sql will contain all of the SQL statements necessary to first create all the tables in your database and then repopulate them.

8. Restoring your Database From the command line: mysql -uusername -ppassword databasename < filename.sql Example: mysql -uroot trii < triibackup.sql Notice you must have already recreated the database in MySQL CREATE DATABASE trii;

9. Inserting Very Large Datasets into your Database You must have a tab-delimited text file (each field in a row is separated with a tab) that contains only the rows from one table. LOAD DATA LOCAL INFILE ‘filename’ INTO TABLE tablename (col1name, col2name,...);

10. Inserting Very Large Datasets into your Database (Continued) You can create a file like this with: SELECT col1name, col2name FROM tablename INTO OUTFILE ‘filename’; Example: SELECT * FROM organism INTO OUTFILE '/tmp/organism.txt';

11. Creating Users/Granting Privileges GRANT ALL ON trii.* TO ‘guest’@’localhost’ IDENTIFIED BY ‘guestpwd’; ALL - privilege type trii.* - all tables in trii database guest - username localhost - machine user can connect from guestpwd - password FLUSH PRIVILEGES;

12. Loading Data from MS Excel We will discuss 2 ways to do this In both cases you should first save your Excel spreadsheet as a tab-delimited text file. Go to: File > Save As

13. Check the File!!! Excel might have saved the end line characters incorrectly. Check in vi. If the file has a bunch of “^M” characters we have to replace them. At the command prompt: >vi gene.txt In vi: :0,$s/^M/^M/g OR At the command prompt: >perl -pi -e ‘s/^M/\n/g’ gene.txt To get the ^M: hold control + v

14. Loading Data from MS Excel Option 1: If your spreadsheet corresponds to a table in your database exactly, then you can save the file as a tab- delimited text file in Excel and then use the SQL command “LOAD DATA LOCAL INFILE…” from before. LOAD DATA INFILE ‘gene.txt’ INTO TABLE gene (ensembl_gene_id, organism_id, name, locuslink, chromosome, chromo_start, chromo_end, description);

15. Loading Data from MS Excel Option 2: Option 2 (most common) If you need to put some Excel columns into one table and some into another use Perl to read in your tab-delimited text file, process your data, and insert it into the database. Remember Perl is great at parsing files!

16. Indexes Add an index on a column (or columns) that will be queried frequently (with an exact match query). If something is a primary key it is automatically indexed. To find out what indexes exist on a table: SHOW INDEX FROM tablename;

17. Indexes Create an index on 1 column: CREATE INDEX indexname ON tablename (columnname); This will make searches on borrower_id fast: CREATE INDEX borrower_index ON on_loan (borrower_id);

18. Indexes Create an index on 2 columns: CREATE INDEX indexname ON tablename (column1name, column2name); This will make queries on book_id fast, as well as queries on book_id and copy_id but NOT copy_id alone: CREATE INDEX book_index ON on_loan (book_id, copy_id);