#!/bin/bash
set -e
test_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
cd ${test_dir}
mkdir -p example
cd example
if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa ]
then
if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz ]
then
docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.2.1 /bin/bash -c \
"cd /mnt/example/ && wget ftp://ftp.ensembl.org/pub/release-75//fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz"
fi
docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.2.1 /bin/bash -c \
"cd /mnt/example/ && gunzip -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz"
fi
if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.fai ]
then
docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.2.1 /bin/bash -c \
"samtools faidx /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa"
fi
rm -rf work_standalone
#Stand-alone NeuSomatic test
docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.2.1 /bin/bash -c \
"python /opt/neusomatic/neusomatic/python/preprocess.py \
--mode call \
--reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
--region_bed /mnt/region.bed \
--tumor_bam /mnt/tumor.bam \
--normal_bam /mnt/normal.bam \
--work /mnt/example/work_standalone \
--scan_maf 0.05 \
--min_mapq 10 \
--snp_min_af 0.05 \
--snp_min_bq 20 \
--snp_min_ao 10 \
--ins_min_af 0.05 \
--del_min_af 0.05 \
--num_threads 1 \
--scan_alignments_binary /opt/neusomatic/neusomatic/bin/scan_alignments"
docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neusomatic:0.2.1 /bin/bash -c \
"CUDA_VISIBLE_DEVICES= python /opt/neusomatic/neusomatic/python/call.py \
--candidates_tsv /mnt/example/work_standalone/dataset/*/candidates*.tsv \
--reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
--out /mnt/example/work_standalone \
--checkpoint /opt/neusomatic/neusomatic/models/NeuSomatic_v0.1.0_standalone_Dream3_70purity.pth \
--num_threads 1 \
--batch_size 100"
docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.2.1 /bin/bash -c \
"python /opt/neusomatic/neusomatic/python/postprocess.py \
--reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
--tumor_bam /mnt/tumor.bam \
--pred_vcf /mnt/example/work_standalone/pred.vcf \
--candidates_vcf /mnt/example/work_standalone/work_tumor/filtered_candidates.vcf \
--output_vcf /mnt/example/work_standalone/NeuSomatic_standalone.vcf \
--work /mnt/example/work_standalone "
rm -rf /mnt/example/work_ensemble
#Ensemble NeuSomatic test
docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.2.1 /bin/bash -c \
"python /opt/neusomatic/neusomatic/python/preprocess.py \
--mode call \
--reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
--region_bed /mnt/region.bed \
--tumor_bam /mnt/tumor.bam \
--normal_bam /mnt/normal.bam \
--work /mnt/example/work_ensemble \
--scan_maf 0.05 \
--min_mapq 10 \
--snp_min_af 0.05 \
--snp_min_bq 20 \
--snp_min_ao 10 \
--ins_min_af 0.05 \
--del_min_af 0.05 \
--num_threads 1 \
--ensemble_tsv /mnt/ensemble.tsv \
--scan_alignments_binary /opt/neusomatic/neusomatic/bin/scan_alignments"
docker run -v ${test_dir}:/mnt -u $UID --memory 30G --shm-size 8G msahraeian/neusomatic:0.2.1 /bin/bash -c \
"CUDA_VISIBLE_DEVICES= python /opt/neusomatic/neusomatic/python/call.py \
--candidates_tsv /mnt/example/work_ensemble/dataset/*/candidates*.tsv \
--reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
--out /mnt/example/work_ensemble \
--checkpoint /opt/neusomatic/neusomatic/models/NeuSomatic_v0.1.0_ensemble_Dream3_70purity.pth \
--num_threads 1 \
--ensemble \
--batch_size 100"
docker run -v ${test_dir}:/mnt -u $UID --memory 30G msahraeian/neusomatic:0.2.1 /bin/bash -c \
"python /opt/neusomatic/neusomatic/python/postprocess.py \
--reference /mnt/example/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
--tumor_bam /mnt/tumor.bam \
--pred_vcf /mnt/example/work_ensemble/pred.vcf \
--candidates_vcf /mnt/example/work_ensemble/work_tumor/filtered_candidates.vcf \
--ensemble_tsv /mnt/ensemble.tsv \
--output_vcf /mnt/example/work_ensemble/NeuSomatic_ensemble.vcf \
--work /mnt/example/work_ensemble"
cd ..
file1=${test_dir}/example/work_standalone/NeuSomatic_standalone.vcf
file2=${test_dir}/NeuSomatic_standalone.vcf
cmp --silent $file1 $file2 && echo "### NeuSomatic stand-alone: SUCCESS! ###" \
|| echo "### NeuSomatic stand-alone FAILED: Files ${file1} and ${file2} Are Different! ###"
file1=${test_dir}/example/work_ensemble/NeuSomatic_ensemble.vcf
file2=${test_dir}/NeuSomatic_ensemble.vcf
cmp --silent $file1 $file2 && echo "### NeuSomatic ensemble: SUCCESS! ###" \
|| echo "### NeuSomatic ensemble FAILED: Files ${file1} and ${file2} Are Different! ###"
Datasets
Models
