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#!/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
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