pg-main from prod server added

pgx-main/get_pgx_result_dev.sh

@@ -0,0 +1,150 @@
+#!/bin/bash
+
+bam_s3_bucket="quantgene-wes-archive"
+upload_s3='true'
+download='true'
+index_bam='true'
+dev_suffix="dev_sref_01"
+stellarpgx_ref="stellar_references/cyp2d6_reference_pgx.bed"
+
+declare -A vcf_s3_dict
+declare -A bam_s3_dict
+
+declare -A stellarpgx_ref_dict=(
+  ["sref_00"]="test3.bed"
+  ["sref_01"]="cyp2d6_reference_pgx.bed"
+  ["sref_02"]="cyp2d6_reference_wes_jan6.bed"
+  ["sref_03"]="cyp2d6_reference_wes_march21.bed"
+)
+
+while getopts ':r:nx' 'OPTKEY'; do
+    case ${OPTKEY} in
+        'r')
+            stellarpgx_ref="stellar_references/"${stellarpgx_ref_dict[$OPTARG]}
+            dev_suffix="dev_"$OPTARG
+            ;;
+        'n')
+            download='false'
+            ;;
+        'x')
+            index_bam='false'
+            ;;
+        '?')
+            echo "INVALID OPTION -- ${OPTARG}" >&2
+            exit 1
+            ;;
+        ':')
+            echo "MISSING ARGUMENT for option -- ${OPTARG}" >&2
+            exit 1
+            ;;
+        *)
+            echo "UNIMPLEMENTED OPTION -- ${OPTKEY}" >&2
+            exit 1
+            ;;
+    esac
+done
+
+echo "----------------------------------------------------------------"
+
+# ------------------------ Start PGx Engine --------------------------
+echo -n "Start Docker container: "
+docker start pgx-api
+
+# ------------------------ Empty data folder -------------------------
+if $download; then
+  if ! [ -z "$(ls -A data)" ]; then
+    echo "Remove existing files in data folder"
+    rm -r data/*
+  fi
+fi
+
+# --------------------- Download files from S3 -----------------------
+while IFS= read vcf_s3; do
+  temp=($(echo $vcf_s3 | tr "/" "\n"))
+  vcf_s3_bucket="${temp[1]}"
+  flowcell="${temp[2]}"
+  run="${temp[3]}"
+  sample="${temp[4]::-4}"
+  
+  vcf_s3_prefix="s3://${vcf_s3_bucket}/${flowcell}/${run}"
+  bam_s3_prefix="s3://${bam_s3_bucket}/${run}"
+  
+  vcf_s3_dict[$sample]=$vcf_s3_prefix
+  bam_s3_dict[$sample]=$bam_s3_prefix
+  
+  bam_s3="${bam_s3_prefix}/${sample}.deduped.bam"
+  if $download; then
+    aws s3 cp $vcf_s3 data/
+    aws s3 cp $bam_s3 data/
+    echo "SAMPLE DOWNLOAD COMPlETE"
+  fi
+done
+echo "ALL DOWNLOADS COMPlETE"
+
+# ------------------------ Index BAM files ---------------------------
+if $index_bam; then
+  for f in data/*.bam; do
+    echo "Indexing: "$f
+    samtools index $f $f".bai"
+  done
+fi
+
+# ------------------------ Run Stellar PGx ---------------------------
+echo "Starting stellar PGx"
+cp $stellarpgx_ref resources/cyp2d6/cyp_hg38/test3.bed
+./run_stellar.sh
+
+# ------------------- Generate final PGx Output ----------------------
+for f in data/*.vcf; do
+  s=${f::-4}
+  printf "\nRun PGx Engine for: ${s:5}\n"
+  python3 combine_outside_calls.py $s
+  curl -X 'POST' \
+    'http://localhost:5000/run' \
+    -H 'accept: application/json' \
+    -H 'Content-Type: multipart/form-data' \
+    -F "files=@${s}.vcf;type=text/x-vcard" \
+    -F "files=@${s}_outside_call.tsv" \
+    -o "${s}_pgx_result.zip"
+done
+
+# ----------------------- Stop PGx Engine ----------------------------
+echo ""
+echo -n "Stop Docker container: "
+docker stop pgx-api
+
+
+# ---------------------- Post-Processing -----------------------------
+if ! [ -z "$(ls -A pgx_results)" ]; then
+  echo "Remove existing files in pgx_results folder"
+  rm -r pgx_results/*
+fi
+echo "Copy PGx Output to pgx_results"
+cp data/*.zip pgx_results/
+
+echo "Unzip and create diplotype/rsid overview"
+python3 create_overview.py
+
+echo "Copy over allele files"
+python3 copy_allele_file.py
+
+rm -r work/*
+rm data/*outside*
+rm data/*zip
+rm data/*.alleles
+
+# --------------------- Upload files to S3 ---------------------------
+if $upload_s3; then
+  for result in $(ls -d pgx_results/*); do
+    sample="${result:12:-11}"
+    vcf_s3_prefix=${vcf_s3_dict[$sample]}
+    bam_s3_prefix=${bam_s3_dict[$sample]}
+    aws s3 cp "${result}/output.json" "${vcf_s3_prefix}/${sample}.${dev_suffix}.json" --storage-class INTELLIGENT_TIERING
+    echo -n "Compressing: "
+    tar -zcvf "${result}.${dev_suffix}.tar.gz" "${result}"
+    aws s3 cp "${result}.${dev_suffix}.tar.gz" "${bam_s3_prefix}/" --storage-class INTELLIGENT_TIERING
+  done
+fi
+
+printf "\nDone\n"
+echo "----------------------------------------------------------------"