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reproduceResults.sh
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#!/bin/bash
#------------------------------------------------------------------------------------------------------------------------
# Name : reproduceResults.sh
# Author : Mathijs A Sanders
# Version : 1.0
# Copyright : None
# Description : reproduceResults.sh -i input_directory -o output_directory [-h]
#------------------------------------------------------------------------------------------------------------------------
display_usage() {
cat << HEREDOC
Usage: reproduceResults.sh -i input_directory -m wgbs_directory -o output_directory [-g reference_genome] [-h]
Required arguments:
-i <input_directory> Input directory containing the JAR file and preprocessed (epi)genomic feature interval files
-o <output_directory> Output directory for storing all downloaded input files, determined tables and RMR output files
HEREDOC
}
#--------------------------------------------------------------------------------------------------
# Get input parameters
#--------------------------------------------------------------------------------------------------
while getopts ':i:o:h' ARG
do
case $ARG in
i)
INPUT_PREFIX=$OPTARG
;;
o)
OUTPUT_PREFIX=$OPTARG
;;
h)
display_usage
exit 0
;;
\?)
echo "Error: Invalid option -$OPTARG (-h for help)"
display_usage
exit -1
;;
esac
done
if [[ -z $INPUT_PREFIX ]]
then
echo "Please specify an input directory containing the RoaMeR JAR file and preprocessed (epi)genomic feature interval files (-h for help)"
exit -1
fi
if [[ -z $OUTPUT_PREFIX ]]
then
echo "Please specify an output directory (-h for help)"
exit -1
fi
if [[ ! -f ${INPUT_PREFIX}/RoaMeR.jar ]]; then
echo "Please specify the input directory containing the RoaMeR JAR file"
exit -1
else
JAR=${INPUT_PREFIX}/RoaMeR.jar
fi
#------------------------------------------------------------------------------------------------
# Download methylation data from GitLab repository
#------------------------------------------------------------------------------------------------
mkdir -p ${OUTPUT_PREFIX}/methylation/
MFILE=${OUTPUT_PREFIX}/methylation/CD34_meth_triplet.txt
if [[ ! -f $MFILE ]]
then
MFILE=${OUTPUT_PREFIX}/methylation/CD34_meth_triplet.txt.gz
wget https://gitlab.wehi.edu.au/flensburg.c/codeForPaper/raw/d10b7b5521ef754a7e2be16f7e221b6790f04762/CD34_meth_triplet.txt.gz -P ${OUTPUT_PREFIX}/methylation/
if [[ ! -f $MFILE ]]
then
echo "Error: Was unable to download the HSPC methylation triplet data from GitLab"
exit -1
else
gunzip ${OUTPUT_PREFIX}/methylation/CD34_meth_triplet.txt.gz
if [[ $? -ne 0 ]]
then
echo "Error: Unable to decompress the HSPC methylation triplet data"
exit -1
fi
fi
fi
MFILE=${OUTPUT_PREFIX}/methylation/CD34_meth_quadruplet.txt
if [[ ! -f $MFILE ]]
then
MFILE=${OUTPUT_PREFIX}/methylation/CD34_meth_quadruplet.txt.gz
wget https://gitlab.wehi.edu.au/flensburg.c/codeForPaper/raw/d10b7b5521ef754a7e2be16f7e221b6790f04762/CD34_meth_quadruplet.txt.gz -P ${OUTPUT_PREFIX}/methylation/
if [[ ! -f $MFILE ]]
then
echo "Error: Was unable to download the HSPC methylation quadruplet data from GitLab"
exit -1
else
gunzip ${OUTPUT_PREFIX}/methylation/CD34_meth_quadruplet.txt.gz
if [[ $? -ne 0 ]]
then
echo "Error: Unable to decompress the HSPC methylation quadruplet data"
exit -1
fi
fi
fi
#------------------------------------------------------------------------------------------------
# Calculate RMR and RMR-CG scores for the (epi)genomic features
#------------------------------------------------------------------------------------------------
mkdir -p ${OUTPUT_PREFIX}/results/Genome_triplet_2B
java -Xmx29G -jar $JAR --analysis rmr --database ${OUTPUT_PREFIX}/methylation/CD34_meth_triplet.txt --bedfiles ${INPUT_PREFIX}/Intervals/Genome/Genome.bed --namesBedFiles Genome --vcfs ${INPUT_PREFIX}/Intervals/VCF/WEHI-AML-1.vcf,${INPUT_PREFIX}/Intervals/VCF/WEHI-AML-2.vcf --sampleNames WEHI-AML-1,WEHI-AML-2 --outputStatistics ${OUTPUT_PREFIX}/results/Genome_triplet_2B/Genome_triplet.txt --outputContext ${OUTPUT_PREFIX}/results/Genome_triplet_2B/Genome_triplet_context.txt --verbose
if [[ $? -ne 0 ]]
then
echo "Error: Error calculating RMR scores for genome-wide triplets"
exit -1
fi
mkdir -p ${OUTPUT_PREFIX}/results/Features_2C
java -Xmx29G -jar $JAR --analysis rmr --database ${OUTPUT_PREFIX}/methylation/CD34_meth_quadruplet.txt --bedfiles ${INPUT_PREFIX}/Intervals/Features/cpgIsland.bed,${INPUT_PREFIX}/Intervals/Features/Promoter.bed,${INPUT_PREFIX}/Intervals/Features/Promoter_flanking.bed,${INPUT_PREFIX}/Intervals/Features/Ensembl_exon.bed,${INPUT_PREFIX}/Intervals/Features/Ensembl_intron.bed --namesBedFiles CpGisland,Promoter,Promoter_flanking,Ensembl_exon,Ensembl_intron --vcfs ${INPUT_PREFIX}/Intervals/VCF/WEHI-AML-1.vcf,${INPUT_PREFIX}/Intervals/VCF/WEHI-AML-2.vcf --sampleNames WEHI-AML-1,WEHI-AML-2 --outputStatistics ${OUTPUT_PREFIX}/results/Features_2C/Features.txt --verbose
if [[ $? -ne 0 ]]
then
echo "Error: Error calculating RMR scores for the (epi)genomic features"
exit -1
fi
mkdir -p ${OUTPUT_PREFIX}/results/Genome_quadruplet_2E
java -Xmx29G -jar $JAR --analysis rmr --database ${OUTPUT_PREFIX}/methylation/CD34_meth_quadruplet.txt --bedfiles ${INPUT_PREFIX}/Intervals/Genome/Genome.bed --namesBedFiles Genome --vcfs ${INPUT_PREFIX}/Intervals/VCF/WEHI-AML-1.vcf,${INPUT_PREFIX}/Intervals/VCF/WEHI-AML-2.vcf --sampleNames WEHI-AML-1,WEHI-AML-2 --outputStatistics ${OUTPUT_PREFIX}/results/Genome_quadruplet_2E/Genome_quadruplet.txt --outputContext ${OUTPUT_PREFIX}/results/Genome_quadruplet_2E/Genome_quadruplet_context.txt --verbose
if [[ $? -ne 0 ]]
then
echo "Error: Error calculating RMR scores for genome-wide quadruplets"
exit -1
fi
mkdir -p ${OUTPUT_PREFIX}/results/Replication_Domain_context_2F
java -Xmx29G -jar $JAR --analysis rmr --database ${OUTPUT_PREFIX}/methylation/CD34_meth_quadruplet.txt --bedfiles ${INPUT_PREFIX}/Intervals/ReplicationDomains/Earliest_Equal.bed,${INPUT_PREFIX}/Intervals/ReplicationDomains/Early_Equal.bed,${INPUT_PREFIX}/Intervals/ReplicationDomains/Late_Equal.bed,${INPUT_PREFIX}/Intervals/ReplicationDomains/Latest_Equal.bed --namesBedFiles Earliest,Early,Late,Latest --vcfs ${INPUT_PREFIX}/Intervals/VCF/WEHI-AML-1.vcf,${INPUT_PREFIX}/Intervals/VCF/WEHI-AML-2.vcf --sampleNames WEHI-AML-1,WEHI-AML-2 --outputStatistics ${OUTPUT_PREFIX}/results/Replication_Domain_context_2F/Replication_domain.txt --outputContext ${OUTPUT_PREFIX}/results/Replication_Domain_context_2F/Replication_domain_context.txt --verbose
if [[ $? -ne 0 ]]
then
echo "Error: Error calculating RMR scores for the replication domains"
exit -1
fi
mkdir -p ${OUTPUT_PREFIX}/results/Strand_bias_Supp5A
java -Xmx29G -jar $JAR --analysis rmr --database ${OUTPUT_PREFIX}/methylation/CD34_meth_quadruplet.txt --bedfiles ${INPUT_PREFIX}/Intervals/Strand/Ensembl_gene_body_strand.bed --namesBedFiles Strand --vcfs ${INPUT_PREFIX}/Intervals/VCF/WEHI-AML-1.vcf,${INPUT_PREFIX}/Intervals/VCF/WEHI-AML-2.vcf --sampleNames WEHI-AML-1,WEHI-AML-2 --outputStatistics ${OUTPUT_PREFIX}/results/Strand_bias_Supp5A/Strand_bias.txt --verbose --stranded
if [[ $? -ne 0 ]]
then
echo "Error: Error calculating RMR scores for the transcriptional strand bias"
exit -1
fi
mkdir -p ${OUTPUT_PREFIX}/results/Expression_strand_bias_Supp5B
java -Xmx29G -jar $JAR --analysis rmr --database ${OUTPUT_PREFIX}/methylation/CD34_meth_quadruplet.txt --bedfiles ${INPUT_PREFIX}/Intervals/Expression_Strand/Expression_none.bed,${INPUT_PREFIX}/Intervals/Expression_Strand/Expression_lowest.bed,${INPUT_PREFIX}/Intervals/Expression_Strand/Expression_low.bed,${INPUT_PREFIX}/Intervals/Expression_Strand/Expression_high.bed,${INPUT_PREFIX}/Intervals/Expression_Strand/Expression_highest.bed --namesBedFiles None,Lowest,Low,High,Highest --vcfs ${INPUT_PREFIX}/Intervals/VCF/WEHI-AML-1.vcf,${INPUT_PREFIX}/Intervals/VCF/WEHI-AML-2.vcf --sampleNames WEHI-AML-1,WEHI-AML-2 --outputStatistics ${OUTPUT_PREFIX}/results/Expression_strand_bias_Supp5B/Expression_strand_bias.txt --verbose --stranded
if [[ $? -ne 0 ]]
then
echo "Error: Error calculating RMR scores for the expression bins"
exit -1
fi
mkdir -p ${OUTPUT_PREFIX}/results/gnomAD_Supp5C
if [[ ! -f ${INPUT_PREFIX}/Intervals/gnomAD/gnomad_0.0001_0.001.vcf ]]
then
if [[ ! -f ${INPUT_PREFIX}/Intervals/gnomAD/gnomad_0.0001_0.001.vcf.gz ]]
then
echo "Error: gnomAD source files do not exist"
exit -1
else
gunzip -c ${INPUT_PREFIX}/Intervals/gnomAD/gnomad_0.0001_0.001.vcf.gz > ${INPUT_PREFIX}/Intervals/gnomAD/gnomad_0.0001_0.001.vcf
fi
fi
java -Xmx29G -jar $JAR --analysis rmr --database ${OUTPUT_PREFIX}/methylation/CD34_meth_quadruplet.txt --bedfiles ${INPUT_PREFIX}/Intervals/ReplicationDomains/Earliest_Equal.bed,${INPUT_PREFIX}/Intervals/ReplicationDomains/Early_Equal.bed,${INPUT_PREFIX}/Intervals/ReplicationDomains/Late_Equal.bed,${INPUT_PREFIX}/Intervals/ReplicationDomains/Latest_Equal.bed --namesBedFiles Earliest,Early,Late,Latest --vcfs ${INPUT_PREFIX}/Intervals/gnomAD/gnomad_0.0001_0.001.vcf --sampleNames gnomAD --outputStatistics ${OUTPUT_PREFIX}/results/gnomAD_Supp5C/gnomAD_Replication_domain.txt --outputContext ${OUTPUT_PREFIX}/results/gnomAD_Supp5C/gnomAD_Replication_domain_context.txt --verbose
if [[ $? -ne 0 ]]
then
echo "Error: Error calculating RMR scores for the replication domains using the rare gnomAD variants"
exit -1
fi
exit 0