regression_clna

#!/usr/bin/env bash

assert() {
  expected=$(echo -ne "${2:-}")
  result="$(eval 2>/dev/null $1)" || true
  result="$(sed -e 's/ *$//' -e 's/^ *//' <<<"$result")"
  if [[ "$result" == "$expected" ]]; then
    return
  fi
  result="$(sed -e :a -e '$!N;s/\n/\\n/;ta' <<<"$result")"
  [[ -z "$result" ]] && result="nothing" || result="\"$result\""
  [[ -z "$2" ]] && expected="nothing" || expected="\"$2\""
  echo "expected $expected got $result for" "$1"
  exit 1
}

set -euxo pipefail

divideBy=$2
subset=$1

i=0
while IFS= read -r line; do
  array[i%$divideBy]+="$line "
  ((++i))
done < <(ls ./regression/*.clna)

for filename in ${array[$subset]}; do
  id=${filename#./regression/*}
  id=${id%*.clna}

  mixcr exportPreset --mixcr-file "regression/${id}.clna" "${id}_preset.yaml"

  mixcr exportClonesPretty "regression/${id}.clna" "${id}_export_clones_pretty.txt"

  mixcr exportClones "regression/${id}.clna" "${id}_export_clones.tsv"

  mixcr exportAlignmentsPretty "regression/${id}.clna" "${id}_export_alignments_pretty.txt"

  mixcr exportAlignments "regression/${id}.clna" "${id}_export_alignments.tsv"

  mixcr exportClonesOverlap "regression/${id}.clna" "${id}_overlap.tsv"

  mixcr exportQc align "regression/${id}.clna" "${id}_qc_align.svg"

  mixcr postanalysis individual --default-downsampling none --default-weight-function none "regression/${id}.clna" "${id}_pa.json"

  if grep -q '\- "assembleContigs"' "${id}_preset.yaml"
  then
    mixcr assembleContigs "regression/${id}.clna" "${id}.contigs.clns"
  fi

  mixcr exportReports "regression/${id}.clna" "${id}_report.txt"

  assert "cat ${id}_report.txt | grep 'file has too old version' | wc -l" "0"
done