DDBJ Annotated Sequence Validator
- 入力: DDBJ (Annotated Seuqnence) 登録形式から変換されたJSON形式
- http://www.ddbj.nig.ac.jp/sub/mss/annotation_file-j.html
- 出力: JSON形式
- https://github.com/ddbj/ddbj_validator/wiki/meeting_20151224#validatorおよびapiレスポンスのjsonデータモデル案
- 機能
- 入力JSONのパース
- ルール情報の取得
- ルール処理実行
- TogoAnnotator
- Error/Warning JSON出力
{
"COMMON": {
"COMMON#feature::DIVISION": {
"location": null,
"qualifiers": [
{
"key": "division",
"value": "HTG"
}
],
"feature": "DIVISION"
},
"COMMON#feature::SUBMITTER": {
"location": null,
"qualifiers": [
{
"key": "ab_name",
"value": "Fujisawa,T."
},
{
"key": "contact",
"value": "Takatomo Fujisawa"
},
{
"key": "email",
"value": "[email protected]"
},
{
"key": "url",
"value": "http://www.bio.nite.go.jp/"
},
{
"key": "phone",
"value": "81-438-52-3951"
},
{
"key": "fax",
"value": "81-438-52-3918"
},
{
"key": "institute",
"value": "National Institute of Technology and Evaluation, NITE"
},
{
"key": "department",
"value": "Bioresource Information Center, Department of Biotechnology"
},
{
"key": "country",
"value": "Japan"
},
{
"key": "state",
"value": "Tokyo"
},
{
"key": "city",
"value": "Shibuya"
},
{
"key": "street",
"value": "2-49-10 Nishihara"
},
{
"key": "zip",
"value": "151-0066"
}
],
"feature": "SUBMITTER"
},
.
.
.
"Chromosome": {
"Chromosome#feature:1..6788435:source": {
"location": "1..6788435",
"qualifiers": [
{
"key": "organism",
"value": "Arthrospira platensis NIES-39"
},
{
"key": "mol_type",
"value": "genomic DNA"
},
{
"key": "strain",
"value": "NIES-39"
},
{
"key": "ff_definition",
"value": "Arthrospira platensis NIES-39 DNA, nearly complete genome"
}
],
"feature": "source"
},
"Chromosome#feature:1..6788435:TOPOLOGY": {
"location": "1..6788435",
"qualifiers": [
{
"key": "circular",
"value": null
}
],
"feature": "TOPOLOGY"
},
"Chromosome#feature:870293..877493:gap": {
"location": "870293..877493",
"qualifiers": [
{
"key": "estimated_length",
"value": "known"
}
],
"feature": "gap"
},
"Chromosome#feature:1018568..1021302:gap": {
"location": "1018568..1021302",
"qualifiers": [
{
"key": "estimated_length",
"value": "known"
}
],
"feature": "gap"
},
"Chromosome#feature:1582613..1585836:gap": {
"location": "1582613..1585836",
"qualifiers": [
{
"key": "estimated_length",
"value": "known"
}
],
"feature": "gap"
},
.
.
.
"Chromosome#feature:152..412:CDS": {
"location": "152..412",
"qualifiers": [
{
"key": "locus_tag",
"value": "NIES39_A00010"
},
{
"key": "codon_start",
"value": "1"
},
{
"key": "transl_table",
"value": "11"
},
{
"key": "product",
"value": "hypothetical protein"
}
],
"feature": "CDS"
},
"Chromosome#feature:complement(377..724):CDS": {
"location": "complement(377..724)",
"qualifiers": [
{
"key": "locus_tag",
"value": "NIES39_A00020"
},
{
"key": "codon_start",
"value": "1"
},
{
"key": "transl_table",
"value": "11"
},
{
"key": "product",
"value": "hypothetical protein"
}
],
"feature": "CDS"
},
.
.
.
}
- 変換スクリプトを作成し以下の操作でJSONを出力
[火 2 23 17:58] tf@~/github/ddbj_validator/misc/tf
%ruby submission_tsv2json ~/Dropbox/apl/DDBJ/NIES39_v17.ddbj > test.json
[月 4 11 14:51] tf@~/github/ddbj_validator/misc/tf
%ruby submission_tsv2json ../../kyulee/sample01_WGS_PRJDB4174.ann
- 設計した入力JSONを利用して、バリデーションスクリプトをperlで実装 ddbj_annotated_sequence_validator.pl
[火 2 23 18:00] tf@~/github/ddbj_validator/misc/tf
%perl ddbj_annotated_sequence_validator.pl
#!/usr/bin/env perl
#
use strict;
use warnings;
use JSON::XS;
use Data::Dumper;
my $input_file = shift || 'test.json';
my $validator = __FILE__;
open my $fh, '<', $input_file
or die "failed to open: $!";
my $input_json = '';
$input_json .= $_ while <$fh>;
my $struct = decode_json($input_json);
#print Dumper $struct;
while (my ($entry, $features) = each(%$struct)){
#print Dumper [$entry, $features];
while(my ($feature_id, $feature) = each(%$features)){
#print Dumper $feature['qualifiers'];
foreach my $qualifier (@{$feature->{'qualifiers'}}){
#print Dumper $qualifier;
if ($qualifier->{'key'} eq 'product'){
exec_togoannotator($qualifier->{'value'});
}
}
}
}
sub exec_togoannotator {
my $product = shift @_;
#TODO: exec togoannotator
my $suggest_product = $product . '_curation';
print <<EOF;
{
\"id\": \"error_code_id\",
\"message\": \"\",
\"message_ja\": \"\",
\"reference\": \"htttp:hoge.org\",
\"level\": \"warning\",
\"method\": $validator,
annotation:
[
{ \"key\": \"biosample package\",
\"source\": \"$input_file\",
\"location\":
\"value\": [\"$product\", \"$suggest_product\"]
}
]
}
EOF
}
DDBJ登録形式ファイルからJSONに変換
ruby misc/tf/submission_tsv2json kyulee/sample01_WGS_PRJDB4174.ann > /tmp/sample01_WGS_PRJDB4174.json
JSONを入力してバリデーターを実行
perl src/annotated_sequence_validator/ddbj_annotated_sequence_validator.pl /tmp/sample01_WGS_PRJDB4174.json
- DDBJ (Annotated Seuqnence) 登録形式から変換されたJSON形式仕様を確定
- validatorをTogoAnnotator実装に合わせてperlで実装
- validatorにTogoAnnotator組み込み【Todo】
- bitbucketレポジトリを配置し、パスを通してTogoAnnotatorモジュールを呼び出す
- validation対象（location）の記法
- 候補、JSONPath - XPath for JSON http://goessner.net/articles/JsonPath/
- 李さん査定バリデーションルールの追加【Todo】
- product qualifierのvalueにホワイトリスト登録以外の単語が使用されていた場合のwarning
- 小菅さん作成の査定用Table形式の入力拡張【Todo】
- ルールJSONの取得
- ルールとメソッドorサブルーチンの対応づけるメタプログラミングな仕組み
- Annotated Seuqenceのルール拡張
- http://www.ddbj.nig.ac.jp/sub/validator-j.html
- 組み合わせのルールについても含めて、BH15.15にて真島さん、李さんと相談