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test_plot_pileup.sh
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#!/bin/bash
RED='\033[0;31m' ; GREEN='\033[0;32m' ; NC='\033[0m' # No Color
die() { echo -e "${RED}$1${NC}" >&2 ; echo ; exit 1 ; } # terminate script
info() { echo ; echo -e "${GREEN}$1${NC}" >&2 ; }
#redirect
verbose=1
exec 3>&1
exec 4>&2
if ((verbose)); then
echo "verbose=1"
else
echo "verbose=0"
exec 1>/dev/null
exec 2>/dev/null
fi
#echo "this should be seen if verbose"
#echo "this should always be seen" 1>&3 2>&4
REL_PATH="$(dirname $0)/"
#...directories files tools arguments commands clean
OUTPUT_DIR="${REL_PATH}/data/out/plot_sig_ref_pileup"
test -d "$OUTPUT_DIR" && rm -r "$OUTPUT_DIR"
mkdir "$OUTPUT_DIR" || die "Failed creating $OUTPUT_DIR"
RAW_DIR="${REL_PATH}/data/raw/plot"
EXP_DIR="${REL_PATH}/data/exp/plot"
testcase_20s() {
[ "${HUMAN_GENOME}" ] || die "Please set the env variable to the human genome path. export HUMAN_GENOME=path/to/file"
GENOME="${HUMAN_GENOME}"
TESTCASE=20.0
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/sorted_eventalign.paf.gz"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT=10
SCALING="znorm"
squigualiser plot_pileup -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" --plot_limit ${PLOT_LIMIT} --sig_scale ${SCALING} && die "testcase:$TESTCASE failed"
TESTCASE=20.1
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/sorted_eventalign.paf.gz"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT=10
REGION="chr1:6,811,011-6,811,198"
SCALING="znorm"
BASE_SHIFT="--base_shift -6"
squigualiser plot_pileup ${BASE_SHIFT} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" --plot_limit ${PLOT_LIMIT} --sig_scale ${SCALING} || die "testcase:$TESTCASE failed"
TESTCASE=20.2
info "testcase:$TESTCASE - reference-signal plot"
GENOME_2="test/data/raw/plot/reference_genomes/chr22_1_5k.fa"
FASTA=${GENOME_2}
SIGNAL="${RAW_DIR}/pileup_view/test_0/na12878_chr22.blow5"
ALIGNMENT="${RAW_DIR}/pileup_view/test_0/na12878_chr22.bam"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT=10
REGION="chr22_1_5k:4000-4500"
SCALING="znorm"
BASE_SHIFT="--base_shift -6"
squigualiser plot_pileup ${BASE_SHIFT} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" --plot_limit ${PLOT_LIMIT} --sig_scale ${SCALING} || die "testcase:$TESTCASE failed"
TESTCASE=20.3
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/sorted_eventalign.paf.gz"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT=10
REGION="chr1:6,811,011-6,811,198"
SCALING="znorm"
BASE_SHIFT="--base_shift -6"
squigualiser plot_pileup --no_overlap ${BASE_SHIFT} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" --plot_limit ${PLOT_LIMIT} --sig_scale ${SCALING} || die "testcase:$TESTCASE failed"
TESTCASE=20.4
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/sorted_eventalign.paf.gz"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT=10
REGION="chr1:6,811,011-6,811,198"
SCALING="znorm"
BASE_SHIFT="--base_shift -6"
squigualiser plot_pileup --overlap_only ${BASE_SHIFT} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" --plot_limit ${PLOT_LIMIT} --sig_scale ${SCALING} || die "testcase:$TESTCASE failed"
TESTCASE=20.5
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/sorted_eventalign.paf.gz"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT=10
REGION="chr1:6,811,011-6,811,198"
SCALING="znorm"
BASE_SHIFT="--base_shift -6"
squigualiser plot_pileup --overlap_only ${BASE_SHIFT} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} --tag_name "testcase-${TESTCASE}" --plot_limit ${PLOT_LIMIT} --sig_scale ${SCALING} && die "testcase:$TESTCASE failed"
TESTCASE=20.6
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/realigned_DNA/reads.blow5"
ALIGNMENT="${RAW_DIR}/realigned_DNA/sorted_test_1.4.bam"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT=10
REGION="chr1:6811404-6811443"
SCALING="znorm"
BASE_SHIFT="--base_shift 0"
squigualiser plot_pileup ${BASE_SHIFT} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" --plot_limit ${PLOT_LIMIT} --sig_scale ${SCALING} || die "testcase:$TESTCASE failed"
TESTCASE=20.7
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/realigned_DNA/reads.blow5"
ALIGNMENT="${RAW_DIR}/realigned_DNA/sorted_test_1.4.bam"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT=10
REGION="chr1:6811404-6811443"
SCALING="znorm"
BASE_SHIFT="--base_shift 0"
squigualiser plot_pileup --plot_reverse ${BASE_SHIFT} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" --plot_limit ${PLOT_LIMIT} --sig_scale ${SCALING} || die "testcase:$TESTCASE failed"
TESTCASE=20.8
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/sorted_eventalign.paf.gz"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT=10
REGION="chr1:6,811,011-6,811,198"
SCALING="znorm"
BASE_SHIFT="--base_shift 0"
squigualiser plot_pileup ${BASE_SHIFT} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" --plot_limit ${PLOT_LIMIT} --sig_scale ${SCALING} || die "testcase:$TESTCASE failed"
TESTCASE=20.8.1
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/sorted_eventalign.paf.gz"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT=10
REGION="chr1:6,811,011-6,811,198"
SCALING="znorm"
BASE_SHIFT="--base_shift 0"
squigualiser plot_pileup --auto --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" --plot_limit ${PLOT_LIMIT} --sig_scale ${SCALING} || die "testcase:$TESTCASE failed"
TESTCASE=20.9
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/sorted_eventalign.paf.gz"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT=10
REGION="chr1:6,811,011-6,811,198"
SCALING="znorm"
PROFILE="--profile kmer_model_dna_r10.4.1_e8.2_400bps_9_mer"
squigualiser plot_pileup ${PROFILE} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" --plot_limit ${PLOT_LIMIT} --sig_scale ${SCALING} || die "testcase:$TESTCASE failed"
TESTCASE=20.10
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/sorted_eventalign.paf.gz"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT=10
REGION="chr1:6,811,011-6,811,198"
SCALING="scaledpA"
PROFILE="--profile kmer_model_dna_r10.4.1_e8.2_400bps_9_mer"
squigualiser plot_pileup ${PROFILE} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" --plot_limit ${PLOT_LIMIT} --sig_scale ${SCALING} || die "testcase:$TESTCASE failed"
}
testcase_21s() {
GENOME="${REL_PATH}/data/raw/plot/reference_genomes/rnasequin_sequences_2.4.fa"
TESTCASE=21.0
info "testcase:$TESTCASE - RNA"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/rna/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/rna/sorted_eventalign.bam"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT="--plot_limit 10"
SCALING="--sig_scale znorm"
squigualiser plot_pileup -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" ${PLOT_LIMIT} ${SCALING} && die "testcase:$TESTCASE failed"
TESTCASE=21.1
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/rna/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/rna/sorted_eventalign.bam"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT="--plot_limit 10"
REGION="R1_92_1:245-284"
SCALING="--sig_scale znorm"
BASE_SHIFT="--base_shift -6"
squigualiser plot_pileup --rna ${BASE_SHIFT} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" ${PLOT_LIMIT} ${SCALING} || die "testcase:$TESTCASE failed"
TESTCASE=21.2
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/rna/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/rna/sorted_eventalign.bam"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT="--plot_limit 10"
REGION="R1_92_1:264-786"
SCALING="--sig_scale znorm"
BASE_SHIFT="--base_shift -6"
squigualiser plot_pileup --rna ${BASE_SHIFT} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" ${PLOT_LIMIT} ${SCALING} || die "testcase:$TESTCASE failed"
TESTCASE=21.3
info "testcase:$TESTCASE - reference-signal plot"
FASTA=${GENOME}
SIGNAL="${RAW_DIR}/f5c_eventalign/rna/reads.blow5"
ALIGNMENT="${RAW_DIR}/f5c_eventalign/rna/sorted_eventalign.bam"
OUTPUT="${OUTPUT_DIR}/testcase_${TESTCASE}"
PLOT_LIMIT="--plot_limit 10"
REGION="R1_92_1:264-786"
SCALING="--sig_scale znorm"
BASE_SHIFT="--base_shift -6"
squigualiser plot_pileup --cprofile --rna ${BASE_SHIFT} --region ${REGION} -f ${FASTA} -s ${SIGNAL} -a ${ALIGNMENT} -o ${OUTPUT} --tag_name "testcase-${TESTCASE}" ${PLOT_LIMIT} ${SCALING} || die "testcase:$TESTCASE failed"
}
testcase_20s #pileup DNA
testcase_21s #pileup RNA
info "all testcases passed"
#rm -r "$OUTPUT_DIR" || die "could not delete $OUTPUT_DIR"
exit 0