Airtran officially completed the merger integration with Southwest Airlines as of Nov 1, 2014. So if you had Airtran credits, they would be transferred to your Rapid Rewards account at a rate of 1 credit=1,200 RR points. I had been waiting for the transfer to occur and it looks like mine have posted to my account so look at yours to see if you have a nice increase in your balance.
The transferred points don’t count towards Companion Pass and are not Tier Qualifying. If your points haven’t yet posted, I would give it another day or 2 since there are lots of customers they have to convert. If you had an Airtran account and not a Southwest account then one was created for you. You may need to call customer service to see what your new account # will be.
Remember that Southwest now flies to some international destinations like Mexico and the Caribbean so put those points to good use for a much needed vacation!