Can I parse hg19.2bit with php?

Question

I know this is possibly an obscure use for php, but I'm working on an idea to navigate the human genome in a rather interesting way.

The problem is I need to know if I can write a php script to parse the freely available data, and if so how would I start? Are there any php scripts to do this in existence?

Answer 1

I'd suggest creating a database design (MySQL) that has the subset of data you want to explore in the PHP application.

Then find a way to upload the data into that data schema. For the uploading part you could use a more poweful language than PHP of your choice, it could be C#, F#, Haskell, or whatever.

This seperation will help simplify things more than doing it all in PHP.

Answer 2

You'll have to write a parser for that, but that should be fairly simple: http://jc.unternet.net/genome/2bitformat.html

And an example in Perl: http://www.perlmonks.org/?node_id=672251