hammerlab/ogene

Name: ogene

Owner: Hammer Lab

Description: Type-safe scripts for genomic file wrangling

Created: 2016-04-21 01:34:31.0

Updated: 2017-02-27 17:04:05.0

Pushed: 2017-02-27 17:04:03.0

Homepage: null

Size: 22

Language: OCaml

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README

What is this?

This is a small program that karyotypically sorts a fasta file.

That is, say you have a fasta file with contigs in lexicographic order, for example, the first contig is 1 (or chr1) and the second is 10, then 11, and so forth; GATK and other tools may not be too happy about this. You can solve this by running this tool:

a-orderer unsorted-fasta.fa sorted-fasta.fa 

You'll likely have to wait a couple minutes (~1 minute for a 3GB fasta on my computer), as the entire fasta is loaded into memory. Sorry.

Now, the contigs will be in order from 1, 2, …, 22, …, X, Y, MT, … and so forth.

And that's all there is to it.

Building

You'll need opam (probably a brew install opam away from you, at most), and then you'll need to do the following:

 deps

Installing these dependencies might take a few minutes; for that, your forgiveness is begged.

From here, you should be good to go.

Contributing

Contributions welcome; please see the Github issues page.

Testing

You'll need to opam testDeps, then run the tests with make all; make test.