I’ve been making scripts/packages with BioJulia packages which read in command line arguments, and I had to write some custom functions to take strings from command line and make Bio.jl types. Well, I’m lazy, ArgParse.jl should just know how to take a command line string and give me a DNA sequence type right? Well turns out it can, you just need to tell it how! BioArgParse.jl will be a package you can use with ArgParse.jl. It will import and extend some ArgParse.jl methods that allow ArgParse.jl to parse any custom type from the command line, and will do this for a growing number of BioJulia types.

Release v0.0.1 lets you pass Biological sequences as command line arguments like:

> julia mystuff.jl --dnaseq atcgatcg

and in your program ArgParse will take them and turn them into BioSequence types.