bio-miga/miga

#!/bin/bash
# Available variables: $PROJECT, $RUNTYPE, $MIGA, $CORES
set -e
SCRIPT="ogs"
# shellcheck source=scripts/miga.bash
. "$MIGA/scripts/miga.bash" || exit 1
DIR="$PROJECT/data/10.clades/03.ogs"

# Initialize
miga_start_project_step "$DIR"

DS=$(miga ls -P "$PROJECT" --ref --no-multi)

if [[ -n $DS ]] ; then
  MIN_ID=$(miga option -P "$PROJECT" --key ogs_identity)
  if [[ ! -s miga-project.ogs ]] ; then
    # Extract RBMs
    if [[ ! -s miga-project.abc ]] ; then
      [[ -d miga-project.tmp ]] || mkdir miga-project.tmp
      for i in $DS ; do
        file="miga-project.tmp/$i.abc"
        [[ -s "$file" ]] && continue
        echo "SELECT seq1,id1,seq2,id2,bitscore from rbm where id >= $MIN_ID;" \
          | sqlite3 "../../09.distances/02.aai/$i.db" | tr "\\|" " " \
          | perl -pe 's/ gene_/ /g' \
          | awk '{ print $1">"$2"'"\\t"'"$3">"$4"'"\\t"'"$5 }' \
          > "$file.tmp"
        mv "$file.tmp" "$file"
      done
      cat miga-project.tmp/*.abc > miga-project.abc
    fi
    rm -rf miga-project.tmp

    # Estimate OGs and Clean RBMs
    ogs.mcl.rb -o miga-project.ogs --abc miga-project.abc -t "$CORES"
    if [[ $(miga option -P "$PROJECT" --key clean_ogs) == "false" ]] ; then
      gzip -9 miga-project.abc
    else
      rm miga-project.abc
    fi
  fi

  # Calculate Statistics
  ogs.stats.rb -o miga-project.ogs -j miga-project.stats
  ogs.core-pan.rb -o miga-project.ogs -s miga-project.core-pan.tsv -t "$CORES"
  Rscript "$MIGA/utils/core-pan-plot.R" \
    miga-project.core-pan.tsv miga-project.core-pan.pdf
else
  touch miga-project.empty
fi

# Finalize
miga_end_project_step "$DIR"