Count occurrences of a string using MySQL

This was originally posted in French here.

There’s no string function in MySQL (and many other databases!) to help you find the number of occurrences of a string within another string.  For example, how many times does « abc »  appear in « abcbcbabcbacbcabcababcabacb » ?

I was asked this question on IRC a long time ago. Some poor soul was trying to find a particular subsequence in a genomic string (for instance « TAT ») in the following sequence :

ATTGGTGGGCTCTACTAAGATATCAACGGGACTTCGGAGCGTGCCGCACTATTT

Obviously, you can use your favorite programming language and do this kind of search programmatically but is there a way to do it in SQL?

Luckily, the answer is yes!  The solution is simple and looks like this:

SELECT FLOOR(( LENGTH(source) - LENGTH(REPLACE(source, target, '')) ) / (LENGTH(target))) as occ

To come back to our example, « source » being the genomic sequence and « target » being « TAT », you’d have :

SELECT FLOOR(( LENGTH('ATTGGTGGGCTCTACTAAGATATCAACGGGACTTCGGAGCGTGCCGCACTATTT') - LENGTH(REPLACE('ATTGGTGGGCTCTACTAAGATATCAACGGGACTTCGGAGCGTGCCGCACTATTT', 'TAT', '')) ) / (LENGTH('TAT'))) as occ

Here’s the answer!

Fortunately, in life there are way more many solutions than problems!  And sometimes, long SQL queries!

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