ncbi-entrez-direct 7.40.20170928+ds-1 / usr / bin / entrez-phrase-search

#!/bin/bash -norc

# simulates phrase search by queries on word pairs that may be indexed in specified field

do_one_query() {
  esearch -db "$database" -query "$*" < /dev/null |
  xtract -pattern ENTREZ_DIRECT -element Count
}

word_at_a_time() {
  sed 's/[^+a-zA-Z0-9]/ /g; s/^ *//' |
  tr 'A-Z' 'a-z' |
  fmt -w 1
}

replace_stop_words() {
  while read line
  do
    case "$line" in
      a | about | again | all | almost | also | although | always | \
      among | an | and | another | any | are | as | at | be | \
      because | been | before | being | between | both | but | by | \
      can | could | did | do | does | done | due | during | each | \
      either | enough | especially | etc | for | found | from | \
      further | had | has | have | having | here | how | however | \
      i | if | in | into | is | it | its | itself | just | kg | km | \
      made | mainly | make | may | mg | might | ml | mm | most | \
      mostly | must | nearly | neither | no | nor | obtained | of | \
      often | on | our | overall | perhaps | pmid | quite | rather | \
      really | regarding | seem | seen | several | should | show | \
      showed | shown | shows | significantly | since | so | some | \
      such | than | that | the | their | theirs | them | then | \
      there | therefore | these | they | this | those | through | \
      thus | to | upon | use | used | using | various | very | was | \
      we | were | what | when | which | while | with | within | \
      without | would )
        echo "+"
        ;;
      * )
        echo "$line"
        ;;
    esac
  done
}

group_phrases() {
  uniq |
  paste -sd "," - |
  sed -e 's/^+//g' -e 's/+$//g' -e 's/,+,/+/g' -e 's/^,//g' -e 's/,$//g' -e 's/+/ /g'
}

word_pairs() {
  while read first rest
  do
    if [ -z "$rest" ]
    then
      echo "$first"
      continue
    fi
    prev=$first
    for curr in $rest
    do
      echo "$prev $curr"
      prev="$curr"
    done
  done
}

get_phrase_counts() {
  echo "$*" |
  word_at_a_time |
  replace_stop_words |
  group_phrases |
  fmt -w 1 |
  tr ',' ' ' |
  word_pairs |
  while read qry
  do
    counts=`do_one_query "\"$qry\" [$field]"`
    if [ $counts -gt 0 ]
    then
      echo "$counts $qry"
    fi
  done
}

make_phrase_search() {
  get_phrase_counts "$@" |
  while read counts qry
  do
    if [ $counts -gt 9 ]
    then
      echo "\"$qry\" [$field]"
    fi
  done | sort -u | tr '\n' '*' | sed -e 's/*$//g' -e 's/*/ AND /g'
}

database="pubmed"
field="TIAB"
mode="search"

while [ $# -gt 0 ]
do
  case "$1" in
    -h | -help | --help )
      mode=help
      break
      ;;
    -db | -database )
      database=$2
      shift
      shift
      ;;
    -field )
      field=$2
      shift
      shift
      ;;
    -count | -counts )
      mode=count
      shift
      ;;
    -string )
      mode=string
      shift
      ;;
    -* )
      exec >&2
      echo "$0: Unrecognized option $1"
      mode=usage
      shift
      ;;
    * )
      break
      ;;
  esac
done

if [ $# -eq 0 ]
then
  mode=usage
fi

case "$mode" in
   help | usage )
     cat <<EOF
USAGE: $0
       [-count|-counts|-string]
       [-db database|-database database]
       [-field field]
       query
EOF
     if [ $mode = usage ]
     then
       exit 1
     fi
     ;;
   count )
     get_phrase_counts "$@" | sed -e 's/^0/-/' | perl -pe 's/\s*(\d+)\s(.+)/$1\t$2/'
     ;;
   search )
     esearch -db "$database" -query "$(make_phrase_search "$@")"
     ;;
   string )
     make_phrase_search "$@"
     ;;
esac