If the output of Trinity is a Fasta file it should be quick to make a simple script to do this. Here are some examples available on Biostars website:

https://www.biostars.org/p/104936/

If you're still having trouble just paste an example of some of the Trinity output and I will try to help you to get a script working.

Thanks Cameron!!

You can find the answer form the website (https://www.biostars.org/p/104936/). Good luck!

Here you have a script that I made yesterday for this exactly same purpose. It doesn't need any external package or third-party libraries. It is written in Perl. Usage is: ./extract_longest_from_trinity Trinity.fasta > Trinity.longest.fasta

Give it a try. Good luck!

(Apparently attachment was removed. I uploaded again without the file extension)