How to parse genebank file using swift for OSX ?

Question

[vytarasov]

I am doing programming for around three months and I am writing programs using swift programming language for OSX. This program supposed to be able to read and write the genbank file. So, my question is how to parse the genbank file to have the functionality to read/write genbank files using swift (if not for swift then for objective-c)?

[Sean Davis]

I suspect that you will need to write your own code to read GenBank files using swift. Swift is not a language that is often used for bioinformatics. Python or perl would be better choices, probably.

[vytarasov]

I know about perl, java an python, but I would like to have the same in swift. Could you give some general tips, directions how I can do this for swift or objective-C?

[Sean Davis]

Hello vytarasov!

It appears that your post has been cross-posted to another site: http://stackoverflow.com/questions/33268884/how-to-parse-genebank-file-i-e-file-with-extension-gb-using-swift-for-osx

This is typically not recommended as it runs the risk of annoying people in both communities.

[vytarasov]

I have removed post from SO.

Answer 1

[lh3]

I doubt you can find genbank file parser in objc, let alone swift. These languages are rarely used in bioinformatics. That said, you can use c/c++ libraries. There should be easy ways to call c functions from swift/objc. With google you can find GBParsy, though I have little idea about its coding quality. Probably ncbi toolbox has a genbank parser, too, but probably it is not easy to use.

If it were me, I would write one by myself.

[vytarasov]

Thanks for suggestions! How difficult would be to write genbank file parser in swift by myself as beginner. Could you give me some advise, some directions, what I should do to write genbank file parser in swift?

[Zhilong Jia]

Maybe read others genbank file parser written by other language you can program.