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#!/bin/sh -e
# http://dep.debian.net/deps/dep8/
# Autopkgtest: Test if QTLtools run analysis correctly
# Author: Dylan Aïssi <bob.dybian@gmail.com>
# Last-Update: 2016-11-16
pkg=qtltools
if [ "$ADTTMP" = "" ] ; then
ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
fi
cd $ADTTMP
cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP
tar Jxvf $ADTTMP/examples.tar.xz
# Mode PCA
QTLtools pca \
--bed genes.50percent.chr22.bed.gz \
--scale \
--center \
--out genes.50percent.chr22
# Mode cis - nominal pass
QTLtools cis \
--vcf genotypes.chr22.vcf.gz \
--bed genes.50percent.chr22.bed.gz \
--cov genes.covariates.pc50.txt.gz \
--nominal 0.01 \
--region chr22:17000000-18000000 \
--out nominals.txt
# Mode cis - permutations pass
QTLtools cis \
--vcf genotypes.chr22.vcf.gz \
--bed genes.50percent.chr22.bed.gz \
--cov genes.covariates.pc50.txt.gz \
--permute 1000 \
--region chr22:17000000-18000000 \
--out permutations.txt
# Mode trans - full pass
QTLtools trans \
--vcf genotypes.chr22.vcf.gz \
--bed genes.simulated.chr22.bed.gz \
--nominal \
--threshold 1e-5 \
--out trans.nominal
# Mode trans - approximate pass
QTLtools trans \
--vcf genotypes.chr22.vcf.gz \
--bed genes.simulated.chr22.bed.gz \
--sample 1000 \
--normal \
--out trans.sample
rm -f $ADTTMP/*
|
