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|
#!/bin/sh
c_red="\033[1;31m"
c_green="\033[1;32m"
c_yellow="\033[1;33m"
c_blue="\033[1;34m"
c_magenta="\033[1;35m"
c_cyan="\033[1;36m"
c_reset="\033[0m"
CLINVAR_URL="https://www.ncbi.nlm.nih.gov/clinvar/"
CLINVAR_RESULTS_XPATH="/html/body/div/div/form/div[1]/div[5]/div/div[5]/div/table/tbody"
CLINVAR_DESC_XPATH="/html/body/div[3]/main/div[4]/div"
CLINVAR_EVID_XPATH="/html/body/div[2]/div[2]/div[3]/table/tbody"
FZF_CMD="fzf --ansi -m --tabstop=1 --bind change:top --layout=reverse --delimiter="\t""
usage() {
printf "Usage: %bclinvar %bsearch-query%b\n" $c_green $c_yellow $c_reset
}
if [ "$#" -eq 0 ] ; then
usage
exit 1
fi
awk_parse_results='
BEGIN{
RS="</tr[^>]*>"
FS="</?td[^>]*>"
OFS="\t"
c_red="\033[1;31m"
c_green="\033[1;32m"
c_yellow="\033[1;33m"
c_blue="\033[1;34m"
c_magenta="\033[1;35m"
c_reset="\033[0m"
}
function getmut(str, res) {
res=gensub(/^.*<span class="ui-button-text">(.*)<\/span>.*$/,"\\1","g",str)
gsub(/>/,">",res)
return striptag(res)
}
function striptag(str) {
gsub(/<[^>]*>/,"",str)
return str
}
function getpath(str) {
str=striptag(str)
if(str~/[pP]athogenic/)
str=c_yellow str c_reset
if(str~/[bB]enign/)
str=c_magenta str c_reset
return str
}
$16~/VCV[0-9]+/{
mut=getmut($4)
if(mut~/^NM/)
print mut, getpath($12), $16
}
'
awk_parse_evidence='
BEGIN{
RS="</tr[^>]*>"
FS="</?td[^>]*>"
OFS="\t"
c_red="\033[1;31m"
c_green="\033[1;32m"
c_yellow="\033[1;33m"
c_blue="\033[1;34m"
c_magenta="\033[1;35m"
c_reset="\033[0m"
}
function striptag(str) {
gsub(/<[^>]*>/,"",str)
return str
}
!done[$4]{
done[$4]++
gsub(/<br\/>/, " ")
gsub(/\n/, " ", $16)
if($8~/[pP]athogenic/)
$8 = c_yellow $8 c_reset
if($8~/[bB]enign/)
$8 = c_magenta $8 c_reset
print $8, $10, $12, $16, $4
print $4, striptag($26) > "/dev/stderr"
}
'
preview() {
id=$(echo "$*" | awk '{id=$NF; gsub(/^VCV/, "", id); print int(id+0)}')
curl -s -L "$CLINVAR_URL/variation/$id" \
--compressed \
| xmllint --html --xpath "$CLINVAR_DESC_XPATH" - 2>/dev/null \
| w3m -dump -T text/html -O utf-8 \
| sed 's/^Help/-------/'
exit 0
}
evid() {
id=$(echo "$*" | awk '{id=$NF; gsub(/^VCV/, "", id); print int(id+0)}')
export EVID_DESC_OUT="evid-$id"
trap "rm $EVID_DESC_OUT" EXIT
curl -s -L "$CLINVAR_URL/variation/$id/evidence/" \
--compressed \
| xmllint --html --xpath "$CLINVAR_EVID_XPATH" - 2>/dev/null \
| awk "$awk_parse_evidence" 2> $EVID_DESC_OUT \
| column -t -s $'\t' \
| $FZF_CMD --preview "sh $0 -VV $EVID_DESC_OUT {}"
exit 0
}
evid_desc() {
db=$1
shift
id=$(echo "%s" "$*" | awk '{print $NF}')
grep "$id" "$db" | awk -F'\t' '{print $2}' | fmt
}
[ "$1" == "-U" ] && preview "$2"
[ "$1" == "-V" ] && evid "$2"
[ "$1" == "-VV" ] && evid_desc "$2" "$3"
# do search
results=$(curl -s -L "$CLINVAR_URL" \
-G --data-urlencode "EntrezSystem2.PEntrez.clinVar.clinVar_Entrez_ResultsPanel.Entrez_DisplayBar.PageSize=200" \
-G --data-urlencode "term=$*" \
--compressed )
parsed_results=$(printf "%s" "$results" | xmllint --html --xpath "$CLINVAR_RESULTS_XPATH" - 2>/dev/null | awk "$awk_parse_results")
if [ "$(printf "%s" "$parsed_results" | wc -l)" -eq 0 ] ; then
parsed_results=$(printf "%s" "$results" | xmllint --html --xpath "/html/body/div[3]/main/div[3]/div/div/dl/dd[5]" - 2>/dev/null | sed 's/<[^>]*>//g')
fi
# Main menu
while : ; do
id=$(printf "%s" "$parsed_results" | column -t -s $'\t' | $FZF_CMD --preview "sh $0 -U {}" | awk '{print $NF}')
[ "$id" = "" ] && exit 0
[ "$id" = "0" ] && exit 0
# xdg-open "$CLINVAR_URL/variation/$id"
sh $0 -V $id
done
|
