5.6 years ago by
No need to develop tools to do this. Many are publicly available for such a common task.
The standard for many years has been Emboss' SeqRet. An online version is here, but I would consider installing the suite if this is something you need to do often. The command line version is as simple as seqret <in> <out>. Wrap it in a loop.
BioPython's SeqIO module can also do this, albeit with a bit more (basic) programming. I'm sure there are equivalents in BioPerl, BioRuby, and via Bioconductor for R.
This kind of task is day one bioinformatics, and the skills required are easy to learn and very straightforward. It's as simple as navigating to a folder and running a program, possibly within the simplest of loops depending on how your data is organized. You are already converting 7000 sequences; it would make sense that you learn about the plethora of resources available to you developed over the past couple decades. You'll also save a ton of time in the future!