It sounds like what you have is a FASTA file.

Click on: CPAN search for fasta and you will get pages of CPAN modules that have something to do with the FASTA format!

I wrote one FASTA parser. Use it if you want. I did this to demo one particular type of parsing technique. There are many other ways to write code that parses a FASTA file.
I don't recommend that you use my code because I think that there is more general purpose code in the way of a CPAN module or "library function" that you can use.

The basic formula for success here is:
Explain what you want to do in terms of:
a) the data that you have now and
b) the information that you want to produce.
And then show
c) your Perl code so far.

I highly recommend trying to understand how to use the BioPerl modules. But in any event, you have not shown either (a) or (b) above. So it is not possible to discuss (c).