#!/bin/bash
set -e
test_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
neusomatic_dir="$( dirname ${test_dir} )"
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
wget ftp://ftp.ensembl.org/pub/release-75//fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz
fi
gunzip -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.gz
fi
if [ ! -f Homo_sapiens.GRCh37.75.dna.chromosome.22.fa.fai ]
then
samtools faidx Homo_sapiens.GRCh37.75.dna.chromosome.22.fa
fi
rm -rf work_standalone
#Stand-alone NeuSomatic test
python ${neusomatic_dir}/neusomatic/python/preprocess.py \
--mode call \
--reference Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
--region_bed ${test_dir}/region.bed \
--tumor_bam ${test_dir}/tumor.bam \
--normal_bam ${test_dir}/normal.bam \
--work 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 ${neusomatic_dir}/neusomatic/bin/scan_alignments
CUDA_VISIBLE_DEVICES= python ${neusomatic_dir}/neusomatic/python/call.py \
--candidates_tsv work_standalone/dataset/*/candidates*.tsv \
--reference Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
--out work_standalone \
--checkpoint ${neusomatic_dir}/neusomatic/models/NeuSomatic_v0.1.0_standalone_Dream3_70purity.pth \
--num_threads 1 \
--batch_size 100
python ${neusomatic_dir}/neusomatic/python/postprocess.py \
--reference Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
--tumor_bam ${test_dir}/tumor.bam \
--pred_vcf work_standalone/pred.vcf \
--candidates_vcf work_standalone/work_tumor/filtered_candidates.vcf \
--output_vcf work_standalone/NeuSomatic_standalone.vcf \
--work work_standalone
rm -rf work_ensemble
#Ensemble NeuSomatic test
python ${neusomatic_dir}/neusomatic/python/preprocess.py \
--mode call \
--reference Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
--region_bed ${test_dir}/region.bed \
--tumor_bam ${test_dir}/tumor.bam \
--normal_bam ${test_dir}/normal.bam \
--work 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 ${test_dir}/ensemble.tsv \
--scan_alignments_binary ${neusomatic_dir}/neusomatic/bin/scan_alignments
CUDA_VISIBLE_DEVICES= python ${neusomatic_dir}/neusomatic/python/call.py \
--candidates_tsv work_ensemble/dataset/*/candidates*.tsv \
--reference Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
--out work_ensemble \
--checkpoint ${neusomatic_dir}/neusomatic/models/NeuSomatic_v0.1.0_ensemble_Dream3_70purity.pth \
--num_threads 1 \
--ensemble \
--batch_size 100
python ${neusomatic_dir}/neusomatic/python/postprocess.py \
--reference Homo_sapiens.GRCh37.75.dna.chromosome.22.fa \
--tumor_bam ${test_dir}/tumor.bam \
--pred_vcf work_ensemble/pred.vcf \
--candidates_vcf work_ensemble/work_tumor/filtered_candidates.vcf \
--ensemble_tsv ${test_dir}/ensemble.tsv \
--output_vcf work_ensemble/NeuSomatic_ensemble.vcf \
--work work_ensemble
cd ..
file1=${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
