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Do you know any good PHP database frameworks that help you build up the query programmatically?

Over the years, we built one in-house at http://qbix.com/platform/guide/database because we couldn't find one. It does things like sharding out of the box, because it's able to understand the query's criteria and target it to the right shards.

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Laravel at least has Query Builder: http://laravel.com/docs/5.1/queries

As an interesting side note: Laravel's AR ORM (=Eloquent) is built on top of the Query Builder so you can leverage Query Builder with AR if you know what you're doing. Can also lead to big problems if you don't realize the possibilities and the caveats.

Like what kind of problems?

Here has been discussion in another comments about overusing ARs for trying to achieve too complicated things that'll lead to DB performance problems. As stated elsewhere here, AR is good for CRUD operations but after that you should use Query Builder or plain SQL to achieve the more complicated cases.

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