genetics-statistics/gemma-wrapper

Name: gemma-wrapper

Owner: genetics-statistics

Description: Caches K between GEMMA runs with LOCO support

Created: 2017-08-27 08:07:42.0

Updated: 2018-05-02 11:25:58.0

Pushed: 2018-05-02 11:25:57.0

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Size: 257

Language: Ruby

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README

GEMMA wrapper caches K between runs with LOCO support

Introduction

GEMMA is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets.

This repository contains gemma-wrapper, essentially a wrapper of GEMMA that provides support for caching the kinship or relatedness matrix (K) and caching LM and LMM computations with the option of full leave-one-chromosome-out genome scans (LOCO).

gemma-wrapper requires a recent version of GEMMA and essentially does a pass-through of all standard GEMMA invocation switches. On return gemma-wrapper can return a JSON object (–json) which is useful for web-services.

Note that this a work in progress (WIP). What is described below should work.

Installation

Prerequisites are

• A recent version of GEMMA
• Standard Ruby >2.0 which comes on almost all Linux systems

gemma-wrapper comes as a Ruby gem and can be installed with

gem install bio-gemma-wrapper

Invoke the tool with

gemma-wrapper --help

and it will render

e: gemma-wrapper [options] -- [gemma-options]
    --loco [x,y,1,2,3...]        Run full LOCO
    --input filen                JSON input variables (used for LOCO)
    --cache-dir path             Use a cache directory
    --json                       Create output file in JSON format
    --force                      Force computation
    --q, --quiet                 Run quietly
-v, --verbose                    Run verbosely
    --debug                      Show debug messages and keep intermediate output
    --                           Anything after gets passed to GEMMA

-h, --help                       display this help and exit

Alternatively, fetch a release of gemma-wrapper

Unpack it and run the tool as

./bin/gemma-wrapper --help

Usage

gemma-wrapper picks up GEMMA from the PATH. To override that behaviour use the GEMMA_COMMAND environment variable, e.g.

env GEMMA_COMMAND=~/opt/gemma/bin/gemma ./bin/gemma-wrapper --help

to pass switches to GEMMA put them after '–' e.g.

gemma-wrapper -v -- -h

prints the GEMMA help

Caching of K

To compute K run the following command from the source directory (so the data files are found):

gemma-wrapper -- \
    -g test/data/input/BXD_geno.txt.gz \
    -p test/data/input/BXD_pheno.txt \
    -gk \
    -debug

Run it twice to see

/tmp/3079151e14b219c3b243b673d88001c1675168b4.log.txt gemma-wrapper CACHE HIT!

gemma-wrapper computes the unique HASH value over the command line switches passed into GEMMA as well as the contents of the files passed in (here the genotype and phenotype files).

You can also get JSON output on STDOUT by providing the –json switch

gemma-wrapper --json -- \
    -g test/data/input/BXD_geno.txt.gz \
    -p test/data/input/BXD_pheno.txt \
    -gk \
    -debug

prints out something that can be parsed with a calling program

rnings":[],"errno":0,"debug":[],"type":"K","files":[["/tmp/18ce786ab92064a7ee38a7422e7838abf91f5eb0.log.txt","/tmp/18ce786ab92064a7ee38a7422e7838abf91f5eb0.cXX.txt"]],"cache_hit":true,"gemma_command":"../gemma/bin/gemma -g test/data/input/BXD_geno.txt.gz -p test/data/input/BXD_pheno.txt -gk -debug -outdir /tmp -o 18ce786ab92064a7ee38a7422e7838abf91f5eb0"}

Note that GEMMA's -o (output) and –outdir switches should not be used. gemma-wrapper stores the cached matrices in TMPDIR by default. If you want something else provide a –cache-dir, e.g.

gemma-wrapper --cache-dir ~/.gemma-cache -- \
    -g test/data/input/BXD_geno.txt.gz \
    -p test/data/input/BXD_pheno.txt \
    -gk \
    -debug

will store K in ~/.gemma-cache.

LOCO

Recent versions of GEMMA have LOCO support for a single chromosome using the -loco switch (for supported formats check https://github.com/genetics-statistics/GEMMA/issues/46). To loop all chromosomes first create all K's with

gemma-wrapper --json \
    --loco 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X -- \
    -g test/data/input/BXD_geno.txt.gz \
    -p test/data/input/BXD_pheno.txt \
    -a test/data/input/BXD_snps.txt \
    -gk \
    -debug > K.json

and next run the LMM's using the K's captured in K.json using the –input switch

gemma-wrapper --json --loco --input K.json -- \
    -g test/data/input/BXD_geno.txt.gz \
    -p test/data/input/BXD_pheno.txt \
    -c test/data/input/BXD_covariates2.txt \
    -a test/data/input/BXD_snps.txt \
    -lmm 2 -maf 0.1 \
    -debug > GWA.json

GWA.json contains the file names of every chromosome

rnings":[],"errno":0,"debug":[],"type":"GWA","files":[["1","/tmp/9e411810ad341de6456ce0c6efd4f973356d0bad.1.assoc.txt.log.txt","/tmp/9e411810ad341de6456ce0c6efd4f973356d0bad.1.assoc.txt.assoc.txt"],["2","/tmp/9e411810ad341de6456ce0c6efd4f973356d0bad.2.assoc.txt.log.txt","/tmp/9e411810ad341de6456ce0c6efd4f973356d0bad.2.assoc.txt.assoc.txt"]...

The -k switch is injected automatically. Again output switches are not allowed (-o, -outdir)

Copyright

Copyright (c) 2017 Pjotr Prins. See LICENSE.txt for further details.