data/motifs/make_annotation.sh
#!/bin/bash
# param -j for JASPAR, -h for HOCOMOCO

echo $1

# check parameters
# JASPAR: source=1, HOCOMOCO: source=2, both : source=0
source=0
if [ $# -eq 1 ]; then
  if [ $1 == "-j" ]; then
    source=1
  elif [ $1 == "-h" ]; then
    source=2
  fi
fi

if [ ${source} -eq 0 ] || [ ${source} -eq 1 ]; then
  echo "### Jaspar (2020) Annotation ###"

  echo "Downloading SQL dump.."

  wget -c http://jaspar.genereg.net/download/database/JASPAR2020.sql.tar.gz --user-agent="Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.8.1.6) Gecko/20070725 Firefox/2.0.0.6"

  echo "Un-tarring it (it isn't actually gzipped).."
  tar xvf JASPAR2020.sql.tar.gz || {
    echo "failed extracting archive"
    exit 1
  }

  echo "Converting to SQLite3.."

  chmod 755 mysql2sqlite
  ./mysql2sqlite JASPAR2020.sql | sqlite3 jaspar.db || {
    echo "failed converting DB to SQLite3"
    exit 1
  }

  echo "Exporting annotation.."

  sqlite3 jaspar.db '.read jaspar_anno_query.sql' | sed -e 's/"//g' >jaspar_anno.csv || {
    echo "failed exporting sql table"
    exit 1
  }

  echo "Cleaning up.."
  rm JASPAR2020.sql jaspar.db JASPAR2020.sql.tar.gz

  echo "Done"

  echo

  echo "Re-creating Mtf file.."
  python3 createMtf.py --jv --jp --ji
fi

if [ ${source} -eq 0 ]; then
  echo
fi

if [ ${source} -eq 0 ] || [ ${source} -eq 2 ]; then
  echo "### Hocomoco Full v11 Annotation ###"
  echo
  echo "Downloading.."
  echo
  echo "Human"
  wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/HUMAN/mono/HOCOMOCOv11_full_annotation_HUMAN_mono.tsv

  echo "Mouse"
  wget -c http://hocomoco11.autosome.ru/final_bundle/hocomoco11/full/MOUSE/mono/HOCOMOCOv11_full_annotation_MOUSE_mono.tsv

  echo "Converting to CSV.."

  echo "TfName,GeneName,Family,UniProt,Source,TaxGroup,Species" >hocomoco_anno.csv
  tail -n+2 HOCOMOCOv11_full_annotation_HUMAN_mono.tsv | awk -F"\t" '{print $1","$2","$14","$19","$8",vertebrates,Homo sapiens"}' | sed -e 's/{.*}//g' >>hocomoco_anno.csv
  tail -n+2 HOCOMOCOv11_full_annotation_MOUSE_mono.tsv | awk -F"\t" '{print $1","$2","$14","$19","$8",vertebrates,Mus musculus"}' | sed -e 's/{.*}//g' >>hocomoco_anno.csv

  echo
  echo "Cleaning up.."
  rm HOCOMOCOv11_full_annotation_HUMAN_mono.tsv
  rm HOCOMOCOv11_full_annotation_MOUSE_mono.tsv

  echo
  echo "Done"

  echo

  echo "Re-creating Mtf file.."
  python3 createMtf.py --hoc
fi
