initial implementation

6 files changed, 242 insertions, 0 deletions

diff --git a/LICENSE b/LICENSE
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+++ b/LICENSE
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+Copyright © 2021 by Justin Bedő
+
+Permission to use, copy, modify, and/or distribute this software for any
+purpose with or without fee is hereby granted, provided that the above
+copyright notice and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR
+IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
diff --git a/README.md b/README.md
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+A command line interface to clinvar.
+
+# Demo
+
+![demo](https://vk3.wtf/clinvar.gif)
+
+# Install
+
+It's just a script, there are dependencies on libxml2 and FZF. If you have
+Nix with flakes enabled you can run it without "installing" by
+```
+nix run git://vk3.wtf/clinvar.git search-terms ...
+```
+or put it into your active profile with
+```
+nix-env -i $(nix eval --raw git://vk3.wtf/clinvar.git)
+```
+
+
+# Contributing
+
+Email me with issues and patches.
diff --git a/clinvar b/clinvar
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+++ b/clinvar
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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(/&gt;/,">",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
diff --git a/clinvar.1 b/clinvar.1
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+++ b/clinvar.1
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+.TH CLINVAR 1
+.SH NAME
+clinvar \- FZF based interface to clinvar for variant searching
+.SH SYNOPSYS
+\fBclinvar\fP \fIterm\fP ...
+.SH DESCRIPTION
+\fBclinvar\fP searches for the given terms in the clinvar database.
+A search is conducted and if multiple results are available they are
+displayed in FZF with a preview of the variant details. A variant
+can be selected to view details of the evidence associated with that
+variant.
+.P
+If a variant is selected, the evidence will be shown in FZF and the
+preview used to show additional free-text description associated with
+the highlighted evidence entry. Cancelling or making a selection will
+return to the search results.
+.SH BUGS
+As the NCBI results navigation is stateful, only the first 200 results
+can be shown. Out of these, only the subset with variant identifiers
+are displayed. This can result in a short list for large queries.
diff --git a/default.nix b/default.nix
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+++ b/default.nix
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+{ lib, stdenvNoCC, fzf, libxml2, makeWrapper }:
+
+stdenvNoCC.mkDerivation {
+  pname = "clinvar";
+  version = "0.1";
+
+  src = ./.;
+
+  nativeBuildInputs = [ makeWrapper ];
+
+  installPhase = ''
+    runHook preInstall
+    install -Dm 755 clinvar $out/bin/clinvar
+    install -Dm 644 clinvar.1 $out/bin/man/man1/clinvar.1
+    runHook postInstall
+  '';
+
+  fixupPhase = ''
+    runHook preFixup
+    wrapProgram $out/bin/clinvar \
+      --prefix PATH : "${lib.makeBinPath [ fzf libxml2 ]}"
+    runHook postFixup
+  '';
+
+  meta.mainProgram = "clinvar";
+}
diff --git a/flake.nix b/flake.nix
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+++ b/flake.nix
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+{
+  inputs.flake-utils.url = "github:numtide/flake-utils";
+
+  outputs = { nixpkgs, flake-utils, self }:
+    flake-utils.lib.eachDefaultSystem (system:
+      let pkgs = nixpkgs.legacyPackages.${system};
+      in rec {
+        packages =
+          flake-utils.lib.flattenTree { clinvar = pkgs.callPackage ./. { }; };
+        defaultPackage = packages.clinvar;
+      });
+}