I have a very long string containing DNA sequence data, which is usually about 500k to 5m characters long.
I want to cut of the first n characters from the beginning and add them to the end of that string.
I need to run that method for approx. 2000 DNA sequences – that’s why i am worried about speed. I don’t want to block my computer for all week.
What is the most efficient way to do that in ruby?
A side-question would be the memory-efficiency. Since i only need to run this task once per sequence, it is not that much important for me, but usually fast does not mean less memory, right? My computer has 2 gigs RAM available(hopefully it is enough).
If you are interested why i need to do this:
The reason why i’d like to do this is, that my source material is analysed for a specific point in the DNA. This point needs to be somewhere in the middle of the DNA for more convenience in later analysis. If this point is to close to the end or to the beginning, i need to split and concat the DNA sequence string.The sequences are circular and the point is the top BLAST hit for dnaA in the bacterial genome (from NCBI database). Since most annotations tend to use the location of the dnaA gene as start, this is pretty annoying if you want to work with the area around that gene.
Sounds interesting!
You can run the rubinius benchmarks and see which method is the most efficient: https://github.com/rubinius/rubinius/tree/master/benchmark/core/string
You don’t have to install rubinius for that but it will give you multithreaded ruby, just like jruby, which might be faster if you have multiple cores on your computer.
To learn how to run the benchmarks check this here: http://rubini.us/doc/en/how-to/write-benchmarks/