Replacing FASTA headers for TopHat & Cufflinks

[brachysclereid]

Hi,

Does anyone know how to replace all the headers in a FASTA file with new names given in another list? The FASTA headers in the genome file are very complex. In the gtf file it just says scaffold1, scaffold2, etc. I need to replace each complex name with the corresponding simple name.

Any tools out there?

[maubp]

It sounds like a straight forward scripting task - can you program in Perl, Python, Ruby, ...?

[brachysclereid]

programming

Thanks,
I was able to solve this problem. I am starting to program. For common tasks like this I just assumed there would be some little program already out there.