greggomann / snp-server

Server for generating nsSNP data

Snp generation server for 1001 proteomes

Installation

make
sudo perl -MCPAN -e 'install Inline::C'

Running

From this root directory

bin/snp_generator.sh <SNPFILES>

If you pass in a list of SNPFILES, it will read those SNP files, otherwise it will look in the default directory for SNPs.

If there are any problems with the execution, search for any files in the work directory that have the extension .error

Important directories

work

The work directory is a WORKING directory, and contains caches of chromosome files after SNPs have been applied to them, etc. This directory can and will be regularly cleaned up/changed.

---

fastas

The fastas directory is an output directory. Here you'll find the finished and translated proteins for each chromosome.

---

out

The out directory contains output from the json-like file creator script, which will summarise all the protein SNPs found for each of the accessions into a single file.

---

ref-data

This contains reference data used for doing the translations. In general, the directory structure is

ref-data
    +--tairX
        +--tairX_cds.txt
        +--tairX_pseudochromosomes
            +--chr1.fas
            +--chr2.fas
            +--chr3.fas
            +--chr4.fas
            +--chr5.fas
            +--chrc.fas
            +--chrm.fas

---

snps

Place any SNP files you want to translate into here. The converter will check to see if it has been translated already, and normally won't do any translation. However, if the timestamp on the SNP file is newer than the timestamp on the output translated files (actually the *.done files found in the work directories), then it will re-do the translation.

SNP file format

The SNPS follow a slightly weird file format. Tab-separated, it is a subset of the GFF file format. All filenames that you put in here should be in lowercase.

#HEADER LINE OF SOME SORT
Chromosome <TAB> position <TAB> original_base <TAB> new_base

For example:

#HEADER LINE OF SOME SORT
Chr1	575	G	T
Chr1	597	C	T
Chr1	603	G	A

Setup on an Amazon EC2 Instance, storing data on S3

S3 Bucket setup

Create a new bucket in S3

BUCKET_ROOT
    +--translated
    +--tair-data
    +--snps
    +--gator-snps

You'll need to set a policy on your bucket to make it world readable

{
	"Version": "2008-10-17",
	"Id": "",
	"Statement": [
		{
			"Sid": "AllowPublicRead",
			"Effect": "Allow",
			"Principal": {
				"AWS": "*"
			},
			"Action": "s3:GetObject",
			"Resource": "arn:aws:s3:::BUCKETNAME/*"
		}
	]
}

Firing up a server

You can back the execution of this using EC2. Start up an instance of the following AMI: ami-6b814f02

Log in to the machine:

Following that, from the snp-server directory:

git pull

make clean && make

bin/make_new_snps.sh BUCKETNAME

The script will prompt you to put in your access credentials from Amazon, and then proceed to generate all the fasta files into your bucket.