My wife is 7 weeks pregnant and when she goes to the bathroom her urine is clear but when she wipes it is really yellow. What could that be?

That sounds like discharge, does she experience any itching or burning sensation down there?

Yes she has itching but no burning

She needs to get to her doctors as she may have a slight case of thrush which is very common during pregnancy. Get to the docs and explain the situation, as soon as you can.
Good luck.

Yup, sounds like a common yeast infection if it is accompanied by itching. Very common in pregnancy.

She needs to wear panties with a cotton crotch and clothes that are not to tight. It would help if she ate yogurt a couple of times a week.