I'd just like to second this solution.

If you are working with sequence data a lot then it's definitely worth investing some time learning the ways of BioPerl.

In addition to its ability to handle a huge variety of data formats, it provides modules to interact with and run numerous sequence analysis packages such as BLAST, EMBOSS and RepeatMasker

Learning the potential of BioPerl combined with the Ensembl Perl API has stood me in very good stead over the years.

Best of luck with your project