\u5909\u7570\u682a\u306e\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u3092\u884c\u3044\u3001\u3044\u304f\u3064\u304b\u5019\u88dc\u3092\u5f97\u308b\u3053\u3068\u304c\u3067\u304d\u307e\u3057\u305f\u3002\n\u6b21\u306f\u539f\u56e0\u907a\u4f1d\u5b50\u306e\u540c\u5b9a\u306b\u9032\u307f\u305f\u3044\u306e\u3067\u3059\u304c\u3001\u65e2\u77e5\u306e\u907a\u4f1d\u5b50\u306e\u30a2\u30ea\u30eb\u304b\u3082\u3057\u308c\u307e\u305b\u3093\u3002\n\u305d\u306e\u5834\u5408\u3001\u5019\u88dc\u907a\u4f1d\u5b50\u3092\u30b5\u30f3\u30ac\u30fc\u6cd5\u3067\u30b7\u30fc\u30af\u30a8\u30f3\u30b9\u3057\u3066\u3001\u65b0\u898f\u3067\u3042\u308b\u3053\u3068\u3092\u78ba\u8a8d\u3057\u3066\u304a\u304d\u305f\u3044\u3068\u3053\u308d\u3067\u3059\u3002\n\u3067\u3059\u304c\u3001\u5019\u88dc\u304c\u8907\u6570\u3042\u3063\u305f\u308a\u3001\u5927\u304d\u304b\u3063\u305f\u308a\u3059\u308b\u3068\u3001\u3044\u304f\u3064\u3082\u306e\u9818\u57df\u306b\u5206\u3051\u3066PCR\u3092\u3057\u3066\u3001\u305d\u308c\u305e\u308c\u3092\u30b7\u30fc\u30af\u30a8\u30f3\u30b9\u3092\u3059\u308b\u5fc5\u8981\u304c\u3042\u308a\u307e\u3059\u3002\n\u307e\u3042\u307e\u3042\u306e\u30b3\u30b9\u30c8\u304c\u304b\u304b\u308a\u307e\u3059\u3002<\/p>\n
Azenta Life Sciences\u3068\u3044\u3046\u4f1a\u793e\u306f\u3001PCR-EZ\u3068\u3044\u3046\u30b5\u30fc\u30d3\u30b9\u3092\u63d0\u4f9b\u3057\u3066\u3044\u307e\u3059\u3002\n\u300c\u5358\u4e00\u306a\u30af\u30ed\u30fc\u30f3\u3067\u76f4\u9396\u72b6\u300dPCR\u7523\u7269\u3092\u3001(\u304a\u305d\u3089\u304f)Nanopore\u3092\u4f7f\u3063\u3066\u30b7\u30fc\u30af\u30a8\u30f3\u30b9\u3057\u3066\u304f\u308c\u308b\u3082\u306e\u3067\u3059\u3002\n1\u30b5\u30f3\u30d7\u30eb\u3042\u305f\u308a4000\u5186(2026\u5e7410\u6708\u73fe\u5728)\u3068\u3001\u30b5\u30f3\u30ac\u30fc\u30b7\u30fc\u30af\u30a8\u30f3\u30b9\u306e10\u56de\u5206\u306b\u3082\u6e80\u305f\u306a\u3044\u4fa1\u683c\u3067\u3059\u3002<\/p>\n
\u3053\u306e\u30b5\u30fc\u30d3\u30b9\u306b\u3001\u3044\u304f\u3064\u304b\u306ePCR\u7523\u7269\u3092\u6df7\u305c\u305f\u3082\u306e\u30921\u30b5\u30f3\u30d7\u30eb\u3068\u3057\u3066\u9001\u4ed8\u3057\u305f\u3068\u3053\u308d\u3001\u30ea\u30fc\u30c9\u304c\u30a2\u30bb\u30f3\u30d6\u30eb\u3055\u308c\u3066\u3001\u3082\u3063\u3068\u3082\u9577\u3044\u9818\u57df\u306b\u3064\u3044\u3066\u306e\u307f\u89e3\u6790\u304c\u3055\u308c\u307e\u3057\u305f\u3002\n\u305d\u3053\u3067\u3001\u751f\u306e\u30ea\u30fc\u30c9(fastq)\u3092\u89e3\u6790\u3057\u3066\u3001\u8907\u6570\u306e\u907a\u4f1d\u5b50\u306e\u5909\u7570\u306e\u6709\u7121\u3092\u8abf\u3079\u308b\u3053\u3068\u306b\u3057\u307e\u3057\u305f\u3002<\/p>\n
\u3053\u306e\u65b9\u6cd5\u306e\u4e00\u3064\u3088\u3044\u3068\u3053\u308d\u306f\u3001\u30d8\u30c6\u30ed\u306e\u633f\u5165\u30fb\u6b20\u5931\u304c\u540c\u5b9a\u3067\u304d\u308b\u3068\u3044\u3046\u3053\u3068\u3067\u3059\u3002\n\u30b5\u30f3\u30ac\u30fc\u6cd5\u306e\u30b7\u30fc\u30af\u30a8\u30f3\u30b9\u3067\u306f\u3050\u3061\u3083\u3050\u3061\u3083\u306b\u306a\u3063\u3066\u8aad\u3081\u306a\u3044\u3068\u3053\u308d\u304c\u3001\u6b21\u4e16\u4ee3\u30b7\u30fc\u30b1\u30f3\u30b5\u30fc\u306f1\u5206\u5b50\u3054\u3068\u306b\u8aad\u3080\u306e\u3067\u3001\u30d8\u30c6\u30ed\u3082\u304d\u308c\u3044\u306b\u8abf\u3079\u308b\u3053\u3068\u304c\u3067\u304d\u307e\u3059\u3002<\/p>\n
(\u7c21\u5358\u306a\u8aac\u660e\u3092\u3044\u305a\u308c\u66f8\u304f)<\/p>\n
\u591a\u6570\u306e\u30ea\u30fc\u30c9\u3092\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u3068\u6bd4\u8f03\u3057\u3066\u3001\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u3092\u4f5c\u6210\u3059\u308b\u3002\u3053\u306e\u90e8\u5206\u306f\u81ea\u5206\u3067\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u66f8\u3051\u306a\u3044\u306e\u3067\u3001\u65e2\u5b58\u306e\u30c4\u30fc\u30eb\u3092\u4f7f\u3046\u3002<\/p>\n
read: ACGTAGAAA-CAGCTATTT\nref : ACGTACAAAACAGGTATTT \n<\/code><\/pre>\n\n- \u89e3\u6790\u30b7\u30b9\u30c6\u30e0\u306e\u524d\u534a\u306f\u30b7\u30fc\u30b1\u30f3\u30b5\u30fc\u306e\u51fa\u529b\u304b\u3089\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u3092\u3064\u304f\u308b\u90e8\u5206\u3002\u5f8c\u534a\u306f\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u304b\u3089\u30ea\u30fc\u30c9\u3092\u6570\u3048\u308b\u90e8\u5206\u306b\u5206\u3051\u308b\u3053\u3068\u304c\u3067\u304d\u308b\u3002<\/li>\n<\/ul>\n
\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u307e\u3067<\/h3>\n
azenta\u306e\u30c7\u30fc\u30bf\u306ffastq\u30d5\u30a1\u30a4\u30eb\u3002nanopore\u306a\u306e\u3067\u3001\u304b\u306a\u308a\u9577\u3044\u3002\u5e73\u5747\u30671000bp\u3050\u3089\u3044\u3002\u30ea\u30fc\u30c9\u6570\u306f\u30b5\u30f3\u30d7\u30eb\u5f53\u305f\u308a600\u5f31\u3002\nbowtie\u3067\u3084\u3063\u3066\u307f\u308b\u30681000bp\u3092\u8d85\u3048\u308b\u30ea\u30fc\u30c9\u306f\u3042\u3066\u3089\u308c\u306a\u3044\u3002\nBLAST\u3092\u4f7f\u3046\u3053\u3068\u306b\u3059\u308b\u3002<\/p>\n
BLAST\u306f\u5165\u529b\u306e\u5f62\u5f0f\u304cfasta\u3002fastq\u304b\u3089fasta\u306b\u5909\u63db\u3059\u308b\u5fc5\u8981\u304c\u3042\u308b\u3002<\/p>\n
\u524d\u534a\u624b\u9806<\/h3>\n\n- BLAST\u306e\u30a4\u30f3\u30c7\u30c3\u30af\u30b9\u3092\u4f5c\u6210\u3059\u308b\u3002makeblastdb -in -out -dbtype nucl \u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u306e\u8d77\u304d\u5834\u6240\u3068\u3001\u30a4\u30f3\u30c7\u30c3\u30af\u30b9\u306e\u8d77\u304d\u5834\u6240\u3092\u6c7a\u3081\u308b\u5fc5\u8981\u304c\u3042\u308b\u3002reference\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u3092\u4f7f\u3046\u3053\u3068\u306b\u3059\u308b\u3002<\/li>\n
- fastq.gz\u3092\u5c55\u958b\u3059\u308b zcat\u306a\u3089\u30d1\u30a4\u30d7\u3067\u3064\u304e\u306e\u51e6\u7406\u3078\u3002\u4e2d\u9593\u30d5\u30a1\u30a4\u30eb\u3092\u3064\u304f\u308b\u306a\u3089gunzip\u3067\u5c55\u958b\u3059\u308b\u3002<\/li>\n
- fasta\u306b\u5909\u63db\u3059\u308b\u30021\u884c\u76ee\u306e\u5148\u982d@\u3092>\u306b\u7f6e\u63db\u3057\u30013\u884c\u76ee\u30684\u884c\u76ee\u3092\u524a\u9664\u3059\u308b\u3002sed\u3092\u4f7f\u3046\u3002\u305d\u3046\u3059\u308b\u3068zcat\u306e\u51fa\u529b\u304b\u3089\u30d1\u30a4\u30d7\u3067sed\u306b\u3064\u306a\u3044\u3067\u3001\u305d\u306e\u307e\u307eblastn\u306b\u3082\u3063\u3066\u3044\u304f\u3053\u3068\u304c\u3067\u304d\u308b\u3002<\/li>\n
- blast\u3067\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u3092\u4f5c\u6210\u3059\u308b\u3002\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u3068\u30ea\u30fc\u30c9\u3092\u6bd4\u8f03\u3059\u308b\u5fc5\u8981\u304c\u3042\u308b\u306e\u3067\u3001-outfmt 5\u306e\u30aa\u30d7\u30b7\u30e7\u30f3\u3092\u3064\u3051\u3066\u3001XML\u3067\u51fa\u529b\u3059\u308b\u3002<\/li>\n<\/ol>\n
\u5f8c\u534a\u624b\u9806<\/h3>\n\n- XML\u304b\u3089\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u90e8\u5206\u3092\u62bd\u51fa\u3059\u308b\u3002\u3053\u3046\u3044\u3046\u306e\u3092\u30d1\u30fc\u30b9(parse)\u3068\u3044\u3046\u3002\u81ea\u5206\u3067\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u66f8\u304f\u306b\u305b\u3088\u3001\u30c4\u30fc\u30eb\u3092\u4f7f\u3046\u306b\u305b\u3088\u3001xpath\u3092\u77e5\u3063\u3066\u304a\u304f\u5fc5\u8981\u304c\u3042\u308b\u3002\u3053\u306e\u5f8c\u3067\u3001\u30ea\u30fc\u30c9\u3092\u6570\u3048\u4e0a\u3052\u308b\u306e\u306b\u90fd\u5408\u306e\u3088\u3044\u5f62\u5f0f\u306b\u5909\u63db\u3059\u308b\u3002<\/li>\n
- \u6570\u3048\u4e0a\u3052\u308b\u3002\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u66f8\u304f\u3002\u3053\u306e\u5f8c\u56f3\u306b\u3059\u308b\u3053\u3068\u3092\u8003\u3048\u308b\u3068R\u3092\u4f7f\u3046\u306e\u304c\u3088\u3044\u304b\u3002<\/li>\n
- R\u3067\u56f3\u3092\u3064\u304f\u308b\u3002<\/li>\n
- \u56f3\u3001\u305d\u306e\u4ed6\u3092\u4e00\u89a7\u3067\u304d\u308b\u3088\u3046\u306bHTML\u3092\u3064\u304f\u308b\u3002<\/li>\n<\/ol>\n
\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u4f5c\u6210\u307e\u3067\u306e\u624b\u9806<\/h2>\nBLAST\u306e\u30a4\u30f3\u30c7\u30c3\u30af\u30b9\u3092\u3064\u304f\u308b<\/h3>\n
\u3068\u308a\u3042\u3048\u305a\u3053\u306e\u30b7\u30b9\u30c6\u30e0\u958b\u767a\u3092\u884c\u3046\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u3092\u3064\u304f\u308a\u3001\u305d\u3053\u306b\u79fb\u52d5\u3059\u308b\u3002\u4ee5\u5f8c\u306f\u305d\u306e\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u3067\u884c\u3046\u3002<\/p>\n
\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3059\u308b\u3002\u30a6\u30a7\u30d6\u304b\u3089\u30d5\u30a1\u30a4\u30eb\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3059\u308b\u306e\u306bcurl\u3092\u4f7f\u3046\u3002-O\u3092\u3064\u3051\u308b\u3068URL\u304b\u3089\u30d5\u30a1\u30a4\u30eb\u540d\u3092\u6c7a\u3081\u3066\u304f\u308c\u308b\u3002<\/p>\n
\n$ curl -O https:\/\/kiku3.tsbio.info\/~takamasa\/260917Honda\/ref\/SUDL.fa\n$ mkdir reference\n$ mv SUDL.fa reference\n<\/pre><\/div>\nblast\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3059\u308b\u3002\n\u30d1\u30c3\u30b1\u30fc\u30b8\u306f apt update; apt search ncbi-blast; \u3067\u63a2\u3059\u3002\napt update\u306f\u30d1\u30c3\u30b1\u30fc\u30b8\u306e\u30c7\u30fc\u30bf\u30d9\u30fc\u30b9\u3092\u66f4\u65b0\u3059\u308b\u30b3\u30de\u30f3\u30c9\u306a\u306e\u3067\u30011\u9031\u9593\u306b1\u56de\u3067\u3082\u3084\u308c\u3070\u5341\u5206\u3002<\/p>\n
\u898b\u3064\u304b\u3063\u305f\u3089 apt install ncbi-blast+ \u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3059\u308b\u3002\n\u7ba1\u7406\u8005\u6a29\u9650\u304c\u5fc5\u8981\u306a\u306e\u3067\u9069\u5b9csudo\u3092\u3064\u3051\u3066\u5b9f\u884c\u3059\u308b\u3002<\/p>\n
\n$ sudo apt update\n$ sudo apt search ncbi-blast\n$ sudo apt install ncbi-blast+\n<\/pre><\/div>\n\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u3092\u4f5c\u6210\u3059\u308b\u3002<\/p>\n
\n$ makeblastdb -in reference\/SUDL.fa -out reference\/SUDL -dbtype nucl\n$ ls reference\nSUDL.fa SUDL.ndb SUDL.nhr SUDL.nin SUDL.not SUDL.nsq SUDL.ntf SUDL.nto\n<\/pre><\/div>\nSUDL.nin\u306a\u3069\u304c\u3067\u304d\u3066\u3044\u308c\u3070\u3088\u3044\u3002<\/p>\n
fastq\u304b\u3089fasta\u3078<\/h3>\n
\u30b5\u30f3\u30d7\u30eb\u30c7\u30fc\u30bf(azenta\u304c\u7d0d\u54c1\u3059\u308b\u30c7\u30fc\u30bf)\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3001\u5c55\u958b\u3059\u308b\u3002<\/p>\n
\n$ curl -O https:\/\/kiku3.tsbio.info\/~takamasa\/260917Honda\/60-1380693045_FASTQ.zip\n$ unzip 60-1380693045_FASTQ.zip\n<\/pre><\/div>\nsed\u3067fastq\u3092fasta\u306b\u52a0\u5de5\u3059\u308b\u30b3\u30de\u30f3\u30c9\u3092\u3064\u304f\u308b\u3002<\/p>\n
\n- 1\u884c\u76ee\u304b\u30894\u884c\u3054\u3068\u306b(1~4)\u3001\u5148\u982d\u306e@\u3092>\u306b\u7f6e\u63db(s\/^@\/>\/)\u3059\u308b\u3002-> 1~4s\/^@\/>\/<\/li>\n
- 3\u884c\u76ee\u304b\u30894\u884c\u3054\u3068\u306b(3~4)\u3001\u884c\u3092\u524a\u9664(d)\u3059\u308b\u3002-> 3~4d<\/li>\n
- 4\u884c\u76ee\u304b\u30894\u884c\u3054\u3068\u306b(4~4)\u3001\u884c\u3092\u524a\u9664(d)\u3059\u308b\u3002-> 4~4d<\/li>\n<\/ol>\n
\u3053\u308c\u3089\u306e\u30b3\u30de\u30f3\u30c9\u3092;\u3067\u3064\u306a\u3050\u3002<\/p>\n
\n$ mkdir tmp\n$ zcat raw_fastq\/2p-7.fastq.gz | sed -e \"1~4s\/^@\/>\/;3~4d;4~4d\" >tmp\/2p-7.fasta\n<\/pre><\/div>\nblast\u691c\u7d22<\/h3>\n
\u5869\u57fa\u914d\u5217\u540c\u58eb\u306e\u691c\u7d22\u306a\u306e\u3067\u3001blastn\u3092\u4f7f\u3046\u3002\u30aa\u30d7\u30b7\u30e7\u30f3\u306e\u610f\u5473\u306f\u4e0b\u8a18\u306e\u901a\u308a\u3002<\/p>\n
\n- -out \u51fa\u529b\u30d5\u30a1\u30a4\u30eb\u540d<\/li>\n
- -outfmt 5 \u51fa\u529b\u5f62\u5f0f\u3092XML\u306b\u3059\u308b<\/li>\n
- -max_target_seqs 1 \u6700\u3082\u4e00\u81f4\u5ea6\u304c\u9ad8\u3044\u914d\u5217\u3060\u3051\u3092\u51fa\u529b\u3059\u308b\u3002<\/li>\n
- -max_hsps 1 \u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u3092\u4e00\u3064\u3060\u3051\u51fa\u529b\u3059\u308b\u3002\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u304c\u74b0\u72b6(\u30d7\u30e9\u30b9\u30df\u30c9)\u306e\u5834\u5408\u3001max_hsps\u306f2\u306b\u3059\u308b\u5fc5\u8981\u304c\u3042\u308b\u304b\u3082\u3057\u308c\u306a\u3044\u3002<\/li>\n<\/ul>\n
\n$ blastn -query tmp\/2p-7.fasta -db reference\/SUDL -out tmp\/2p-7.xml -outfmt 5 -max_target_seqs 1 -max_hsps 1\n<\/pre><\/div>\n\u691c\u7d22\u7d50\u679c\u306f\u3053\u3093\u306a\u611f\u3058<\/p>\n
\n \n<Iteration>\n <Iteration_iter-num>1<\/Iteration_iter-num>\n <Iteration_query-ID>Query_1<\/Iteration_query-ID>\n <Iteration_query-def>97b33a7e-4236-4a9c-9ceb-ff9b41540e2c runid=cde8f4c2-9722-4978-885d-aca7c6634fc5 ch=990 start_time=2026-09-16T21:44:48.358392+09:00 flow_cell_id=PBI88494 basecall_gpu=NVIDIA_A800_80GB_PCIe protocol_group_id=20260916-RUN1-PBI88494-Japan_KK sample_id= barcode=barcode89 barcode_alias=barcode89 parent_read_id=97b33a7e-4236-4a9c-9ceb-ff9b41540e2c basecall_model_version_id=dna_r10.4.1_e8.2_400bps_sup@v5.2.0<\/Iteration_query-def>\n <Iteration_query-len>937<\/Iteration_query-len>\n<Iteration_hits>\n<Hit>\n <Hit_num>1<\/Hit_num>\n <Hit_id>gnl|BL_ORD_ID|1<\/Hit_id>\n <Hit_def>SUDL2<\/Hit_def>\n <Hit_accession>1<\/Hit_accession>\n <Hit_len>5430<\/Hit_len>\n <Hit_hsps>\n <Hsp>\n <Hsp_num>1<\/Hsp_num>\n <Hsp_bit-score>1583.7<\/Hsp_bit-score>\n <Hsp_score>857<\/Hsp_score>\n <Hsp_evalue>0<\/Hsp_evalue>\n <Hsp_query-from>1<\/Hsp_query-from>\n <Hsp_query-to>937<\/Hsp_query-to>\n <Hsp_hit-from>4761<\/Hsp_hit-from>\n <Hsp_hit-to>3822<\/Hsp_hit-to>\n <Hsp_query-frame>1<\/Hsp_query-frame>\n <Hsp_hit-frame>-1<\/Hsp_hit-frame>\n <Hsp_identity>918<\/Hsp_identity>\n <Hsp_positive>918<\/Hsp_positive>\n <Hsp_gaps>13<\/Hsp_gaps>\n <Hsp_align-len>945<\/Hsp_align-len>\n <Hsp_qseq>GAGAATTCTACATGTATCTGGTGAAACACTCCTGTAAATCAATATCAGGTCTCGCTACTGAAGAAAAACATGAATGGTTAAAAGTTGAGCCTGCAAAGAGAAAACAAGAACTAAGGTGTAATGTGCTATGAGCAGAGCTTGATCATGAAAAACATAAGAAAATTGATACTCTAAAGCAGAATTCTCTTCCTTGCTCAACACATTCACAACTCTCTTCAAGATAACTTCAATAGGCTGGTCGAGCATTTTCAACCGCTTTGGAGATGGCTTGCCATTTCTCGCCATGCTTCGGCTCACAAGCTACACACTTCGCCACAACTTCCTTCCTGTCCTCATCAGAGCCATGTTGAAGTTGAAGATTGCTTAAACAACGCCCAGAAATCGCCAATATCTGGGCGAGCGGTAACAGCACGTTCAAACCATGCTCTGGCTTTCTCCACCTTCTTGTCTTGCCAAAAGAGCTTGGCAACAGCTATGGTGACATAGA-GGTCGCGATCACACTTCTTCATAGCATCAATACTCTTTGTTTTCCGT-GAGGGACGTGGCGCCATCTCAATGTCCGCAGCCCAGAGGATACCACTCTTGGGACAGTCTTGCAGAGCCTTTGACATCAAGTGCTCTGCTTCTCTCTTGTTGTCATGCCTCAGTTCAGCGCGAATAGCAGCTAACCATAGCTCAGCCCCCC-AGGATTCTTCTTCCTGGCCGTAGT-AGA-TAGCC-GAGCTTTGTT-AGCCCCATTCACTTTCTCTTCAAGATCAGCGAGTGAGAGCCACAGTGGTATGCAGTGGGGACAGTGCTTCAAACCAGTGTCATAAGCTTTCCTGGCCTGTTCTAGATGCTTGAACCATTTGTGGAGCT-CCCAAGCATTAACCAAAGCTTGAAGAATGTTGGGAATTGCTTCAAACCTTCATTAAGCAATCTCCTCTCCTCCTCTACGTTG<\/Hsp_qseq>\n <Hsp_hseq>GAGAATTCTACATGTATCTGGTGAAACACTCCTGTAAATCAATATCAGGTCTCGCTACTGAAGAAAAACATGAATGGTTAAAAGTTGAGCCTGCAAAGAGAAAACAAGAACTAAGGTGTAATGTGCTATGAGCAGAGCTTGATCATGAAAAACATAAGAAAATTGATACTCTCAAGCAGAATTCTCTTCCTTGCTCAACGCATTCACAACTCTCTTCAAGATAACTTCAATAGGCTGGT-GAGCATTTTCAACCGCTTTGGAGATGGCTTGCCATTTCTCGCCATGCTTCGGCTCACAAGCTACACACTTCGCCACAACTTCCTTCCTGTCCTCATCAGAGCCATGTTGAAGTTCAA-ATTTGTAGAACAACGCCCAGAAATCGCCAATATCTGGGCCAACGGTAACAGCACGTTCAAACCATGCTCTGGCTTTCTCCACCTTCTTGTCTTGCCAAAAGAGCTTGGCAACAGCTATGGTGACAT-GAGGGTCGCGATCACACTTCTTCATAGCATCAATACTCTTTGTTTTCCGTCGA-GGACGTGGCGCCATCTCAATGTCCGCAGCCCAGAGGATACCACTCTTGGGACAGTCTTGCAGAGCCTTTGACATCAAGTGCTCTGCTTCTCTCTTGTTGTCATGCCTCAGTTCAGCGCGAATAGCAGCTAACCATAGCTCAGCCCCCCCAGGATTCTTCTTCCTGGCCGTGGTGAGAATAGCCCGAGCTTTGTTTAG-CCCATTCACTTTCTCTTCAAGATCAGCGAGTGAGAGCCACAGTGGTATGCAGTGGGGACAGTGCTTCAAACCAGTGTCATAAGCTTTCCTGGCCTGTTCTAGATGCTTGAACCGTTCCTCGAGCTGCCCAAGCATTAACCAAAGCTTGAAGAATGTTGGGAATTGCTTCAAACCTTCATTAAGCAATCTCCTCTCCTCCTCTACGTTG<\/Hsp_hseq>\n <Hsp_midline>|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||| | ||||||||||||||||||||||||||||||| | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||| || ||| ||||| |||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || | ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||<\/Hsp_midline>\n <\/Hsp>\n <\/Hit_hsps>\n<\/Hit>\n<\/Iteration_hits>\n <Iteration_stat>\n <Statistics>\n <Statistics_db-num>4<\/Statistics_db-num>\n <Statistics_db-len>24161<\/Statistics_db-len>\n <Statistics_hsp-len>16<\/Statistics_hsp-len>\n <Statistics_eff-space>22193337<\/Statistics_eff-space>\n <Statistics_kappa>0.46<\/Statistics_kappa>\n <Statistics_lambda>1.28<\/Statistics_lambda>\n <Statistics_entropy>0.85<\/Statistics_entropy>\n <\/Statistics>\n <\/Iteration_stat>\n<\/Iteration>\n<\/pre>\n<\/div>\n\u5f8c\u534a<\/h2>\n\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u3068\u4f4d\u7f6e\u60c5\u5831\u3092\u53d6\u308a\u51fa\u3059<\/h3>\n
BLAST\u304c\u51fa\u529b\u3057\u305fXML\u306e\u4e2d\u304b\u3089\u5fc5\u8981\u306a\u60c5\u5831\u3092\u629c\u304d\u51fa\u3059\u3002<\/p>\n
\u30ea\u30fc\u30c9\u3054\u3068\u306bIteration\u304c\u3064\u304f\u3089\u308c\u3001\u305d\u306e\u4e2d\u306bHit\u304c\u3042\u308b\u3002Hit_def\u304c\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u5074\u306e\u5869\u57fa\u914d\u5217\u306e\u540d\u524d\u3067\u3001Hit_hsps\u304c\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u3092\u793a\u3059\u3002\nHsp_query-from\u306bBLAST\u3067\u3044\u3046\u3068\u3053\u308d\u306e\u30af\u30a8\u30ea\u30fc\u306e\u4f4d\u7f6e\u60c5\u5831\u304c\u3042\u308a\u3001\u3053\u308c\u304c\u30ea\u30fc\u30c9\u306e\u4e00\u81f4\u3057\u305f\u90e8\u5206\u306e\u59cb\u307e\u308a\u4f4d\u7f6e\u3002Hsp_hit-from\u304c\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u5074\u306e\u4f4d\u7f6e\u3002\n\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u306f Hsp_qseq\u3068Hsp_hseq\u306b\u3042\u308b\u3002<\/p>\n
\u3053\u308c\u3089\u306e\u60c5\u5831\u3092\u629c\u304d\u51fa\u3057\u3001\u6b21\u306e\u51e6\u7406\u306b\u6301\u3063\u3066\u3044\u304d\u3084\u3059\u3044\u5f62\u306b\u6574\u3048\u308b\u5fc5\u8981\u304c\u3042\u308b\u306e\u3067\u3001\u30d7\u30ed\u30b0\u30e9\u30e0\u3092\u4f5c\u6210\u3059\u308b\u3002\n\u3069\u306e\u3088\u3046\u306a\u8a00\u8a9e\u3067\u3064\u304f\u3063\u3066\u3082\u3088\u3044\u304c\u3001\u4eca\u56de\u306f\u79c1\u306e\u5f97\u610f\u306aPHP\u3067\u884c\u3046\u3002<\/p>\n
XML\u3092\u7c21\u5358\u306b\u6271\u3048\u308b\u3088\u3046\u306b\u3059\u308bsimplexml\u3092\u4f7f\u3046\u306e\u3067\u3001php-xml\u3082\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3059\u308b\u5fc5\u8981\u304c\u3042\u308b\u3002<\/p>\n
\n$ sudo apt install php-cli php-xml\n<\/pre><\/div>\n<\/p>\n
\n scripts\/parse_blastxml.php<\/h5>\n\n#!\/usr\/bin\/php\n<?php\n\/* \u30b3\u30de\u30f3\u30c9\u30e9\u30a4\u30f3\u306e\u5f15\u6570\u306f $argv \u306b\u5165\u3063\u3066\u3044\u308b\u3002\n * \u4e00\u3064\u76ee\u306e\u5f15\u6570\u304c\u5b58\u5728\u3057\u3001\u8aad\u8fbc\u53ef\u80fd\u306a\u30d5\u30a1\u30a4\u30eb\u3067\u3042\u308c\u3070xml\u3068\u3057\u3066\u8aad\u307f\u8fbc\u3080\u3002\n * \u7121\u3044\u5834\u5408\u306f\u3001\u6a19\u6e96\u5165\u529b\u3092\u8aad\u307f\u8fbc\u3080\n *\/\nif(isset($argv[1]) && file_exists($argv[1])){\n $xml = simplexml_load_file($argv[1]);\n}else{\n $xml = simplexml_load_string(stream_get_contents(STDIN));\n}\n \n\/\/ Hit\u3068\u3044\u3046\u30bf\u30b0\u3092\u63a2\u3059\nforeach($xml->xpath('.\/\/Hit') as $xhit){\n \n \/\/ Hit_def\u3068\u3044\u3046\u30bf\u30b0\u306e\u5024\u3092$values\u306b\u3044\u308c\u308b\n $values = ['subject' => (string) $xhit->{"Hit_def"}];\n \n \/\/ Hsp\u3068\u3044\u3046\u30bf\u30b0\u3092\u63a2\u3059\n foreach($xhit->xpath('.\/\/Hsp') as $xhsp){\n \n \/\/ Hsp_hit-from\u306a\u3069\u306e\u5024\u3092\u53d6\u308a\u51fa\u3059\u3002\u5148\u982d\u306eHsp_\u306f\u5171\u901a\u306a\u306e\u3067\u3001\u307e\u3068\u3081\u3066\u3064\u3051\u308b\n foreach(['hit-from', 'hit-to', 'query-from', 'query-to', 'qseq', 'hseq'] as $key){\n $values[$key] = (string) $xhsp->{"Hsp_$key"};\n }\n \n \/\/ \u5024\u3092\u3064\u306a\u3052\u3066\u51fa\u529b\u3059\u308b\n echo join("\\t", array_values($values)) . "\\n";\n }\n \n}\n<\/pre>\n<\/div>\nblast\u306f\u30af\u30a8\u30ea\u30fc\u306e\u5411\u304d\u306b\u30b5\u30d6\u30b8\u30a7\u30af\u30c8\u3092\u305d\u308d\u3048\u308b\u3002\u4eca\u56de\u306f\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u3092\u57fa\u6e96\u306b\u30ea\u30fc\u30c9\u3092\u4e26\u3079\u305f\u3044\u306e\u3067\u3001\u9006\u5411\u304d\u306e\u5834\u5408\u306f\u76f8\u88dc\u9396\u306b\u5909\u63db\u3059\u308b\u5fc5\u8981\u304c\u3042\u308b\u3002\u305d\u306e\u305f\u3081\u306e\u51e6\u7406\u3092\u52a0\u3048\u308b\u3002<\/p>\n
<\/p>\n
\n scripts\/parse_blastxml.php<\/h5>\n\n<?php\n\/* \u30b3\u30de\u30f3\u30c9\u30e9\u30a4\u30f3\u306e\u5f15\u6570\u306f $argv \u306b\u5165\u3063\u3066\u3044\u308b\u3002\n * \u4e00\u3064\u76ee\u306e\u5f15\u6570\u304c\u5b58\u5728\u3057\u3001\u8aad\u8fbc\u53ef\u80fd\u306a\u30d5\u30a1\u30a4\u30eb\u3067\u3042\u308c\u3070xml\u3068\u3057\u3066\u8aad\u307f\u8fbc\u3080\u3002\n * \u7121\u3044\u5834\u5408\u306f\u3001\u6a19\u6e96\u5165\u529b\u3092\u8aad\u307f\u8fbc\u3080\n *\/\nif(isset($argv[1]) && file_exists($argv[1])){\n $xml = simplexml_load_file($argv[1]);\n}else{\n $xml = simplexml_load_string(stream_get_contents(STDIN));\n}\n \n\/\/ Hit\u3068\u3044\u3046\u30bf\u30b0\u3092\u63a2\u3059\nforeach($xml->xpath('.\/\/Hit') as $xhit){\n \n \/\/ Hit_def\u3068\u3044\u3046\u30bf\u30b0\u306e\u5024\u3092$values\u306b\u3044\u308c\u308b\n $values = ['subject' => (string) $xhit->{"Hit_def"}];\n \n \/\/ Hsp\u3068\u3044\u3046\u30bf\u30b0\u3092\u63a2\u3059\n foreach($xhit->xpath('.\/\/Hsp') as $xhsp){\n \n \/\/ Hsp_hit-from\u306a\u3069\u306e\u5024\u3092\u53d6\u308a\u51fa\u3059\u3002\u5148\u982d\u306eHsp_\u306f\u5171\u901a\u306a\u306e\u3067\u3001\u307e\u3068\u3081\u3066\u3064\u3051\u308b\n foreach(['hit-from', 'hit-to', 'query-from', 'query-to', 'qseq', 'hseq'] as $key){\n $values[$key] = (string) $xhsp->{"Hsp_$key"};\n }\n \n if(intval($values['hit-to']) < intval($values['hit-from'])){\n $values['hseq'] = complement($values['hseq']);\n $values['qseq'] = complement($values['qseq']);\n swap($values['hit-from'], $values['hit-to']);\n swap($values['query-from'], $values['query-to']);\n }\n \n \/\/ \u5024\u3092\u3064\u306a\u3052\u3066\u51fa\u529b\u3059\u308b\n echo join("\\t", array_values($values)) . "\\n";\n }\n \n}\n \n\/* \u76f8\u88dc\u9396\u5909\u63db\u3059\u308b\u95a2\u6570 *\/\nfunction complement($seq){\n $replace = [\n 'AaCc' => '1234',\n 'TtGg' => 'AaCc',\n '1234' => 'TtGg',\n ];\n foreach($replace as $from => $to){\n $seq = strtr($seq, $from, $to);\n }\n \n $rev = '';\n for($i = 0 ; $i < strlen($seq) ; $i ++){\n $rev = $seq[$i] . $rev;\n }\n return $rev;\n}\n \n\/* \u5024\u3092\u5165\u308c\u66ff\u3048\u308b *\/\nfunction swap(&$a, &$b){\n $buf = $b;\n $b = $a;\n $a = $buf;\n}\n<\/pre>\n<\/div>\n\u3053\u3093\u306a\u611f\u3058\u3067\u5b9f\u884c\u3059\u308b\u3002<\/p>\n
\n$ php scripts\/parse_blastxml.php tmp\/2p-7.xml >tmp\/2p-7.aln\n<\/pre><\/div>\n\u30ea\u30fc\u30c9\u3092\u6570\u3048\u308b<\/h3>\n
R\u3067\u884c\u3046\u3002<\/p>\n
read: 1 CGCCTAAA....GTCATACA 4224\nref : 2937 CGCCTAAA....GTCATACA 1286\n<\/code><\/pre>\n\u3053\u3046\u3044\u3046\u30c7\u30fc\u30bf\u304b\u3089<\/p>\n
2937 C\n2938 G\n2939 C\n...\n<\/code><\/pre>\n\u3068\u3044\u3046\u30c7\u30fc\u30bf\u3092\u3064\u304f\u308b\u3002<\/p>\n
\u96e3\u3057\u3044\u306e\u306f<\/p>\n
read: 937 CAA-CGTAGAGGGAG....ATTCTC 1\nref : 3822 CAAACGTAGAGG-AG....ATTCTC 4761\n<\/code><\/pre>\n\u3053\u3046\u3044\u3046\u30c7\u30fc\u30bf\u3067\u3001\u30ae\u30e3\u30c3\u30d7\u304c\u3042\u308b\u3068\u304d\u306b\u3069\u3046\u51e6\u7406\u3059\u308b\u306e\u304b\u3068\u3044\u3046\u3053\u3068\u3002<\/p>\n
\u30ea\u30fc\u30c9\u5074\u306e\u6b20\u5931\u306f – \u3068\u3044\u3046\u5869\u57fa\u306b\u7f6e\u63db\u3055\u308c\u305f\u3053\u3068\u306b\u3059\u308b\u3002\n\u30ea\u30fc\u30c9\u5074\u306e\u633f\u5165\u306f\u4e00\u3064\u524d\u306e\u5869\u57fa\u3068\u3064\u306a\u3052\u3066\u3001G -> GG \u3068\u3044\u3046\u7f6e\u63db\u3068\u3057\u3066\u51e6\u7406\u3059\u308b\u3002<\/p>\n
\u4e0a\u8a18\u306e\u4f8b\u3060\u3068\u3001<\/p>\n
3822 C\n3823 A\n3824 A\n3825 -\n3826 C\n3827 G\n3828 T\n3829 A\n3830 G\n3831 A\n3832 G\n3833 GG\n3834 A\n<\/code><\/pre>\n\u3068\u66f8\u304d\u51fa\u3059\u3053\u3068\u306b\u3059\u308b\u3002<\/p>\n
BLAST\u306e\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u304c\u633f\u5165\u3092\u3069\u3046\u3044\u308c\u308b\u306e\u304b\u3068\u3044\u3046\u3068\u3053\u308d\u307e\u3067\u8abf\u6574\u3067\u304d\u3066\u3044\u306a\u3044\u306e\u3067\u3001\u76f8\u88dc\u9396\u5909\u63db\u3057\u305f\u3068\u304d\u306e\u30ae\u30e3\u30c3\u30d7\u306e\u4f4d\u7f6e\u304c\u305a\u308c\u3066\u3044\u308b\u53ef\u80fd\u6027\u304c\u3042\u308b\u3002\n\u4eca\u5f8c\u554f\u984c\u306b\u306a\u3063\u305f\u3068\u304d\u306b\u8003\u3048\u308b<\/p>\n
\u307e\u305a\u306fR\u3067\u8aad\u307f\u8fbc\u3093\u3067\u307f\u308b\u3002\u305d\u306e\u305f\u3081\u306bR\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3002<\/p>\n
\n$ sudo apt install r-base-core\n<\/pre><\/div>\n\u30b7\u30f3\u30d7\u30eb\u306a\u30c7\u30fc\u30bf\u3092\u4f7f\u3063\u3066\u3001\u8a08\u7b97\u65b9\u6cd5\u3092\u8003\u3048\u308b<\/p>\n
\n$ R # R\u3092\u8d77\u52d5\n\n# \u633f\u5165\u3068\u6b20\u5931\u3068\u30df\u30b9\u30de\u30c3\u30c1\u304c1\u3064\u305a\u3064\u3042\u308b\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u3092\u7528\u610f\u30021\u884c\u3060\u3051\u306e\u8868\u3068\u3057\u3066\u30c7\u30fc\u30bf\u3092\u4f5c\u6210\n> d1 <- data.frame('SUDL2', 1, 10, 1, 10, 'AAATTCC-GG', 'AA-TTTCCGG')\n\n# \u5217\u540d\u3092\u3064\u3051\u308b\n> names(d1) <- c('subject', 'hfrom', 'hto', 'qfrom', 'qto', 'hseq', 'qseq')\n\n# \u30c7\u30fc\u30bf\u3092\u78ba\u8a8d\n> d1\n subject hfrom hto qfrom qto hseq qseq\n1 SUDL2 1 10 1 10 AAATTCC-GG AA-TTTCCGG\n\n# \u4e00\u6587\u5b57\u305a\u3064\u5206\u5272\u3059\u308b\n> strsplit(d1$hseq, '')\n[[1]]\n [1] "A" "A" "A" "T" "T" "C" "C" "-" "G" "G"\n\n# \u30ea\u30b9\u30c8\u306b\u306a\u3063\u3066\u3044\u308b\u306e\u3067\u3001\u305d\u308c\u3092\u3068\u308a\u3060\u3059\n> hseq <- strsplit(d1$hseq, '')[[1]]\n> hseq\n [1] "A" "A" "A" "T" "T" "C" "C" "-" "G" "G"\n \n# \u30ea\u30fc\u30c9\u5074\u3082\u540c\u3058\u3088\u3046\u306b\u51e6\u7406\n> qseq <- strsplit(d1$qseq, '')[[1]]\n> qseq\n [1] "A" "A" "-" "T" "T" "T" "C" "C" "G" "G"\n\n# \u5869\u57fa\u306e\u4f4d\u7f6e\u3092\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u3092\u57fa\u6e96\u306b\u3064\u304f\u308b\n# \u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u5074\u304c-\u306e\u5834\u5408\u3001\u4f4d\u7f6e\u3092\u5897\u3084\u3055\u306a\u3044\u65b9\u6cd5\u3092\u8003\u3048\u308b\n> hseq != '-'\n [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE\n\n# TRUE\u304c1\u3001FALSE\u304c0\u3068\u3057\u3066\u3001\u7d2f\u7a4d\u548c\u3092\u6c42\u3081\u308b\n> cumsum(hseq != '-')\n [1] 1 2 3 4 5 6 7 7 8 9\n\n# \u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u5074\u306e\u30a2\u30e9\u30a4\u30e1\u30f3\u30c8\u958b\u59cb\u4f4d\u7f6e\u304b\u3089\u3001\u5869\u57fa\u4f4d\u7f6e\u3092\u8a08\u7b97\u3059\u308b\n> d1$hfrom - 1 + cumsum(hseq != '-')\n [1] 1 2 3 4 5 6 7 7 8 9\n> hpos <- d1$hfrom - 1 + cumsum(hseq != '-')\n\n# \u5869\u57fa\u306e\u4f4d\u7f6e\u3054\u3068\u306b\u30ea\u30fc\u30c9\u5074\u306e\u6587\u5b57\u5217\u3092\u7d50\u5408\u3059\u308b\u3002\n> tapply(qseq, hpos, paste, collapse = '')\n 1 2 3 4 5 6 7 8 9\n "A" "A" "-" "T" "T" "T" "CC" "G" "G"\n> q <- tapply(qseq, hpos, paste, collapse = '')\n\n# \u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u5074\u306f\u30ae\u30e3\u30c3\u30d7\u306a\u3057\u306b\u306a\u308b\u3088\u3046\u306b-\u3092\u524a\u9664\u3059\u308b\u3002\n> hseq[hseq == '-'] <- ''\n> tapply(hseq, hpos, paste, collapse = '')\n 1 2 3 4 5 6 7 8 9\n"A" "A" "A" "T" "T" "C" "C" "G" "G"\n> h <- tapply(hseq, hpos, paste, collapse = '')\n\n# \u30ea\u30fc\u30c9\u304c\u30ab\u30d0\u30fc\u3059\u308b\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u3092\u3064\u304f\u3063\u305f\u3002\n> q == h\n 1 2 3 4 5 6 7 8 9\n TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE TRUE\n<\/pre>\n<\/div>\n\u3053\u308c\u3092\u30ea\u30fc\u30c9\u3054\u3068\u306b\u51e6\u7406\u3057\u3066\u3001\u907a\u4f1d\u5b50\u3054\u3068\u306b\u6570\u3048\u308b<\/p>\n
<\/p>\n
\n scripts\/count_read.R<\/h5>\n\n# Rscript script.R alignment \u3068\u3044\u3046\u3088\u3046\u306b\u51e6\u7406\u5bfe\u8c61\u3092\u5f15\u6570\u3067\u6e21\u3057\u305f\u3044\u3002\n# \u305d\u308c\u3092\u53d6\u5f97\u3059\u308b\u305f\u3081\u306e\u95a2\u6570 commandArgs\u3002\nargv <- commandArgs(trailingOnly = T)\n \n# \u30bf\u30d6\u533a\u5207\u308a\u30c6\u30ad\u30b9\u30c8\u3092\u8aad\u307f\u8fbc\u3080\nd1 <- read.delim(argv[1], header = F, stringsAsFactor = F)\n \n# \u5217\u306b\u540d\u524d\u3092\u3064\u3051\u308b\u3002\u3053\u308c\u306f\u524d\u306ePHP\u306e\u51e6\u7406\u3068\u5bfe\u5fdc\u3055\u305b\u308b\nnames(d1) <- c('subject', 'hfrom', 'hto', 'qfrom', 'qto', 'hseq', 'qseq')\n \n# split(d1, d1$subject) \u3067d1\u306e\u30c7\u30fc\u30bf\u3092subject\u5217\u3001\u3064\u307e\u308a\u907a\u4f1d\u5b50\u3054\u3068\u306b\u5206\u3051\u308b\u3002\n# lapply \u306f\u6700\u521d\u306e\u5f15\u6570\u306e\u30ea\u30b9\u30c8\u3092\u500b\u5225\u306b\u30012\u756a\u76ee\u306e\u5f15\u6570\u306e\u95a2\u6570\u306b\u6e21\u3059\ncounts <- lapply(split(d1, d1$subject), function (dr){\n \n # d1\u306e\u4e00\u3064\u76ee\u306e\u907a\u4f1d\u5b50\u306e\u30c7\u30fc\u30bf\u304cdr\u3068\u3057\u3066\u6e21\u3055\u308c\u3066\u3044\u308b\n # \u4eca\u5ea6\u306f\u305d\u308c\u30921\u884c\u3054\u3068\u306b\u51e6\u7406\u3059\u308b\u3002rownames(dr) \u306f\u884c\u540d\u3067\u3001\u4eca\u56de\u306fread.delim\u3057\u305f\u6642\u70b9\u3067\u306e\u884c\u756a\u53f7(\u3064\u307e\u308a\u91cd\u8907\u304c\u306a\u3044)\n d2 <- lapply(split(dr, rownames(dr)), function (ds){\n # hseq\u3092\u7a7a\u6587\u5b57''\u3067\u5206\u5272\u3059\u308b\u3002\u3064\u307e\u308a1\u6587\u5b57\u3054\u3068\u306b\u5206\u3051\u3089\u308c\u308b\u3002strsplit\u306f\u914d\u5217\u306b\u5bfe\u3057\u3066\u4f5c\u7528\u3057\u3001\u8fd4\u308a\u5024\u306f\u30ea\u30b9\u30c8\u306b\u306a\u3063\u3066\u3044\u308b\u3002\u3053\u3053\u3067\u306fds$hseq\u306f\u8981\u7d20\u304c1\u3064\u306e\u914d\u5217\u306a\u306e\u3067\u3001[[1]]\u3092\u3064\u3051\u3066\u30ea\u30b9\u30c8\u3067\u306a\u304f\u3057\u3066\u3044\u308b\u3002\n hseq <- strsplit(ds$hseq, '')[[1]]\n qseq <- strsplit(ds$qseq, '')[[1]]\n \n # hseq\u304c'-'\u3067\u306a\u3051\u308c\u3070\u3001true(1)\u3001-\u306a\u3089\u3070false(0)\u306b\u3059\u308b\u3002\u3053\u308c\u3092\u7d2f\u7a4d\u548c(cumsum)\u3059\u308b\u3053\u3068\u3067\u3001\u30ae\u30e3\u30c3\u30d7\u3092\u30b9\u30ad\u30c3\u30d7\u3057\u3064\u3064\u4f4d\u7f6e\u60c5\u5831\u3092\u5f97\u308b\n hpos <- ds$hfrom - 1 + cumsum(hseq != '-')\n \n # \u30ea\u30fc\u30c9\u306e\u914d\u5217\u3092\u3001\u4f4d\u7f6e\u60c5\u5831\u6bce\u306b\u3001paste\uff08\u6587\u5b57\u5217\u9023\u7d50)\u3059\u308b\u3002collapse = ''\u3068\u3059\u308b\u3053\u3068\u3067\u3001\u914d\u5217\u3092\u7d50\u5408\u3059\u308b ('A', 'C') -> 'AC' \u306b\u306a\u308b\u3002\n q <- tapply(qseq, hpos, paste, collapse = '')\n \n hseq[hseq == '-'] <- ''\n h <- tapply(hseq, hpos, paste, collapse = '')\n q == h\n })\n pos <- unlist(lapply(d2, names))\n match <- unlist(d2, use.names = F)\n res <- cbind(total = table(pos), match = tapply(match, pos, sum))\n res[order(as.numeric(rownames(res))),]\n})\n<\/pre>\n<\/div>\n\u3053\u306e\u30c7\u30fc\u30bf\u3092\u6b21\u306e\u51e6\u7406\u306b\u3069\u3046\u3082\u3063\u3066\u3044\u304f\u306e\u304b\u3092\u8003\u3048\u308b\u3002<\/p>\n
\n- \u3053\u306e\u51e6\u7406\u306e\u7d9a\u304d\u3068\u3057\u3066\u30b0\u30e9\u30d5\u3092\u66f8\u304f\u3002\n
\n- \u30e1\u30ea\u30c3\u30c8: \u4e2d\u9593\u30d5\u30a1\u30a4\u30eb\u306e\u5f62\u5f0f\u3092\u8003\u3048\u306a\u304f\u3066\u3088\u3044\u3002<\/li>\n
- \u30c7\u30e1\u30ea\u30c3\u30c8: \u305f\u3076\u3093\u3053\u308c\u306f\u305d\u308c\u306a\u308a\u306b\u91cd\u3044(\u6642\u9593\u304c\u304b\u304b\u308b)\u51e6\u7406\u306a\u306e\u3067\u3001\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u691c\u8a3c\u306b\u6642\u9593\u304c\u304b\u304b\u308b\u3002<\/li>\n<\/ul>\n<\/li>\n
- R\u306e\u30aa\u30d6\u30b8\u30a7\u30af\u30c8\u3068\u3057\u3066\u66f8\u304d\u51fa\u3059\u3002\n
\n- \u30e1\u30ea\u30c3\u30c8: \u30ea\u30b9\u30c8\u306a\u3069\u8907\u96d1\u306a\u5f62\u5f0f\u306e\u30c7\u30fc\u30bf\u304c\u305d\u306e\u307e\u307e\u3082\u3063\u3066\u3044\u3051\u308b\u3002<\/li>\n
- \u30c7\u30e1\u30ea\u30c3\u30c8: \u4f5c\u3089\u308c\u305f\u30d5\u30a1\u30a4\u30eb\u306e\u4e2d\u8eab\u3092\u77e5\u308b\u3053\u3068\u304c\u3067\u304d\u306a\u3044\u3002<\/li>\n<\/ul>\n<\/li>\n
- \u30c6\u30ad\u30b9\u30c8\u3068\u3057\u3066\u66f8\u304d\u51fa\u3059\u3002\n
\n- \u30e1\u30ea\u30c3\u30c8: \u8a08\u7b97\u7d50\u679c\u3092\u78ba\u8a8d\u3067\u304d\u308b\u3002<\/li>\n
- \u30c7\u30e1\u30ea\u30c3\u30c8: \u8907\u96d1\u306a\u30c7\u30fc\u30bf\u3092\u66f8\u304d\u51fa\u3059\u3068\u3001\u8aad\u8fbc\u306e\u51e6\u7406\u304c\u9762\u5012\u3002<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n
\u4eca\u56de\u306fR\u306e\u30aa\u30d6\u30b8\u30a7\u30af\u30c8\u306e\u307e\u307e\u4fdd\u5b58\u3059\u308b\u3053\u3068\u306b\u3059\u308b\u3002\n\u62e1\u5f35\u5b50\u3001Robj\u306e\u4fdd\u5b58\u5148\u3092\u30b9\u30af\u30ea\u30d7\u30c8\u306e2\u756a\u76ee\u306e\u5f15\u6570\u3068\u3057\u3066\u6e21\u3059\u3002<\/p>\n
\n scripts\/count_read.R<\/h5>\n\n# Rscript script.R alignment \u3068\u3044\u3046\u3088\u3046\u306b\u51e6\u7406\u5bfe\u8c61\u3092\u5f15\u6570\u3067\u6e21\u3057\u305f\u3044\u3002\n# \u305d\u308c\u3092\u53d6\u5f97\u3059\u308b\u305f\u3081\u306e\u95a2\u6570 commandArgs\u3002\nargv <- commandArgs(trailingOnly = T)\n \n# \u30bf\u30d6\u533a\u5207\u308a\u30c6\u30ad\u30b9\u30c8\u3092\u8aad\u307f\u8fbc\u3080\nd1 <- read.delim(argv[1], header = F, stringsAsFactor = F)\n \n# \u5217\u306b\u540d\u524d\u3092\u3064\u3051\u308b\u3002\u3053\u308c\u306f\u524d\u306ePHP\u306e\u51e6\u7406\u3068\u5bfe\u5fdc\u3055\u305b\u308b\nnames(d1) <- c('subject', 'hfrom', 'hto', 'qfrom', 'qto', 'hseq', 'qseq')\n \n# split(d1, d1$subject) \u3067d1\u306e\u30c7\u30fc\u30bf\u3092subject\u5217\u3001\u3064\u307e\u308a\u907a\u4f1d\u5b50\u3054\u3068\u306b\u5206\u3051\u308b\u3002\n# lapply \u306f\u6700\u521d\u306e\u5f15\u6570\u306e\u30ea\u30b9\u30c8\u3092\u500b\u5225\u306b\u30012\u756a\u76ee\u306e\u5f15\u6570\u306e\u95a2\u6570\u306b\u6e21\u3059\ncounts <- lapply(split(d1, d1$subject), function (dr){\n \n # d1\u306e\u4e00\u3064\u76ee\u306e\u907a\u4f1d\u5b50\u306e\u30c7\u30fc\u30bf\u304cdr\u3068\u3057\u3066\u6e21\u3055\u308c\u3066\u3044\u308b\n # \u4eca\u5ea6\u306f\u305d\u308c\u30921\u884c\u3054\u3068\u306b\u51e6\u7406\u3059\u308b\u3002rownames(dr) \u306f\u884c\u540d\u3067\u3001\u4eca\u56de\u306fread.delim\u3057\u305f\u6642\u70b9\u3067\u306e\u884c\u756a\u53f7(\u3064\u307e\u308a\u91cd\u8907\u304c\u306a\u3044)\n d2 <- lapply(split(dr, rownames(dr)), function (ds){\n # hseq\u3092\u7a7a\u6587\u5b57''\u3067\u5206\u5272\u3059\u308b\u3002\u3064\u307e\u308a1\u6587\u5b57\u3054\u3068\u306b\u5206\u3051\u3089\u308c\u308b\u3002strsplit\u306f\u914d\u5217\u306b\u5bfe\u3057\u3066\u4f5c\u7528\u3057\u3001\u8fd4\u308a\u5024\u306f\u30ea\u30b9\u30c8\u306b\u306a\u3063\u3066\u3044\u308b\u3002\u3053\u3053\u3067\u306fds$hseq\u306f\u8981\u7d20\u304c1\u3064\u306e\u914d\u5217\u306a\u306e\u3067\u3001[[1]]\u3092\u3064\u3051\u3066\u30ea\u30b9\u30c8\u3067\u306a\u304f\u3057\u3066\u3044\u308b\u3002\n hseq <- strsplit(ds$hseq, '')[[1]]\n qseq <- strsplit(ds$qseq, '')[[1]]\n \n # hseq\u304c'-'\u3067\u306a\u3051\u308c\u3070\u3001true(1)\u3001-\u306a\u3089\u3070false(0)\u306b\u3059\u308b\u3002\u3053\u308c\u3092\u7d2f\u7a4d\u548c(cumsum)\u3059\u308b\u3053\u3068\u3067\u3001\u30ae\u30e3\u30c3\u30d7\u3092\u30b9\u30ad\u30c3\u30d7\u3057\u3064\u3064\u4f4d\u7f6e\u60c5\u5831\u3092\u5f97\u308b\n hpos <- ds$hfrom - 1 + cumsum(hseq != '-')\n \n # \u30ea\u30fc\u30c9\u306e\u914d\u5217\u3092\u3001\u4f4d\u7f6e\u60c5\u5831\u6bce\u306b\u3001paste\uff08\u6587\u5b57\u5217\u9023\u7d50)\u3059\u308b\u3002collapse = ''\u3068\u3059\u308b\u3053\u3068\u3067\u3001\u914d\u5217\u3092\u7d50\u5408\u3059\u308b ('A', 'C') -> 'AC' \u306b\u306a\u308b\u3002\n q <- tapply(qseq, hpos, paste, collapse = '')\n \n hseq[hseq == '-'] <- ''\n h <- tapply(hseq, hpos, paste, collapse = '')\n q == h\n })\n pos <- unlist(lapply(d2, names))\n match <- unlist(d2, use.names = F)\n res <- cbind(total = table(pos), match = tapply(match, pos, sum))\n res[order(as.numeric(rownames(res))),]\n})\n \n# \u4fdd\u5b58\u3059\u308b\nsave('counts', file = argv[2])\n<\/pre>\n<\/div>\n\u3053\u3093\u306a\u611f\u3058\u3067\u5b9f\u884c\u3059\u308b\u3002<\/p>\n
\n$ Rscript scripts\/count_read.R tmp\/2p-7.aln tmp\/2p-7.Robj\n<\/pre><\/div>\n\u56f3\u306b\u3059\u308b<\/h3>\n
\u4e0a\u8a18\u3067\u5869\u57fa\u3054\u3068\u306b\u30ea\u30fc\u30c9\u6570\u3068\u30df\u30b9\u30de\u30c3\u30c1\u3092\u6570\u3048\u308b\u3053\u3068\u304c\u3067\u304d\u305f\u3002\u3053\u308c\u3092\u56f3\u306b\u3059\u308b\u3002\n\u907a\u4f1d\u5b50\u6bce\u306b\u56f3\u306b\u3057\u3064\u3064\u3001\u7e2e\u5c3a\u3092\u305d\u308d\u3048\u305f\u3044\u3002<\/p>\n
\u7e2e\u5c3a\u3092\u63c3\u3048\u308b\u3068\u3044\u3046\u3053\u3068\u306f\u3001\u907a\u4f1d\u5b50\u306e\u9577\u3055\u306e\u60c5\u5831\u304c\u5fc5\u8981\u3067\u3001\u305d\u308c\u306f\u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u304b\u3089\u8aad\u307f\u8fbc\u3080\u3053\u3068\u306b\u3059\u308b\u3002<\/p>\n
\n \n# \u30ea\u30d5\u30a1\u30ec\u30f3\u30b9(FASTA)\u3092\u8aad\u307f\u8fbc\u3080\nreadFasta <- function (file) {\n buf <- scan(file, what = 'c')\n ref <- sapply(split(buf, cumsum(substr(buf, 1, 1) == '>')), function (single) {\n name <- strsplit(single[1], '[[:space:]]')[[1]][1]\n name <- substring(name, 2)\n seq <- paste(single[-1], collapse = '')\n c('name' = name, 'seq' = seq)\n })\n data.frame(t(ref))\n}\n<\/pre>\n<\/div>\n\u51fa\u529b\u3059\u308b\u30d5\u30a1\u30a4\u30eb\u540d\u3092\u5f15\u6570\u3067\u4e0e\u3048\u308b\u5fc5\u8981\u304c\u3042\u308b\u3002<\/p>\n
\n \nlapply(names(counts), function (gene){\n png(paste0(base_name, gene, ".png"))\n})\n<\/pre>\n<\/div>\n\u3068\u3044\u3046\u3068\u3053\u308d\u3092\u8003\u3048\u308b\u3068\u3001\u5f15\u6570\u306b\u306freference.fa\u3068\u3001\u753b\u50cf\u306e\u30d5\u30a1\u30a4\u30eb\u540d\u304c\u5fc5\u8981\u3068\u3044\u3046\u3053\u3068\u306b\u306a\u308b\u3002<\/p>\n
<\/p>\n
\n scripts\/pile.R<\/h5>\n\n# \u5f15\u6570 Rojb reference.fa image_path (.gene_name.png\u3092\u52a0\u3048\u308b)\nargv <- commandArgs(trailingOnly = T)\n \nload(argv[1]) # counts\u304c\u8aad\u307f\u8fbc\u307e\u308c\u308b\n \n# \u30ea\u30d5\u30a1\u30ec\u30f3\u30b9(FASTA)\u3092\u8aad\u307f\u8fbc\u3080\nreadFasta <- function (file) {\n buf <- scan(file, what = 'c')\n ref <- sapply(split(buf, cumsum(substr(buf, 1, 1) == '>')), function (single) {\n name <- strsplit(single[1], '[[:space:]]')[[1]][1]\n name <- substring(name, 2)\n seq <- paste(single[-1], collapse = '')\n c('name' = name, 'seq' = seq)\n })\n data.frame(t(ref))\n}\n \nref <- readFasta(argv[2])\n \nmax_len <- max(nchar(ref$seq))\nmax_height <- max(sapply(counts, function (count){\n max(count[,'total'])\n}))\n \nlapply(names(counts), function (gene){\n png(paste0(argv[3], '.', gene, '.png'), width = 1024, height = 300)\n count <- counts[[gene]]\n plot(as.numeric(rownames(count)), count[,'total'],\n xlim = c(1, max_len), ylim = c(1, max_height),\n type = 'h', col = 'green', \n xlab = 'position', ylab = 'count', main = gene\n )\n points(as.numeric(rownames(count)), count[,'total'] - count[,'match'], type = 'h', col = 'red')\n dev.off()\n})\n<\/pre>\n<\/div>\n\u6b21\u306e\u3088\u3046\u306b\u5b9f\u884c\u3059\u308b\u3002<\/p>\n
\n$ Rscript scripts\/pile.R tmp\/reference.fa tmp\/2p-7.Robj\n<\/pre><\/div>\n\u30ec\u30dd\u30fc\u30c8\u3092\u4f5c\u6210<\/h3>\n
\u56f3\u3092\u4e00\u89a7\u8868\u793a\u3059\u308bindex.html\u3092\u4f5c\u6210\u3059\u308b\u3002<\/p>\n
<\/p>\n
\n scripts\/make_html.php<\/h5>\n\n<?php\n\/* \u30b3\u30de\u30f3\u30c9\u30e9\u30a4\u30f3\u306e\u5f15\u6570\u306f $argv \u306b\u5165\u3063\u3066\u3044\u308b\u3002\n * \u4e00\u3064\u76ee\u306e\u5f15\u6570\u304c\u5b58\u5728\u3057\u3001\u8aad\u8fbc\u53ef\u80fd\u306a\u30d5\u30a1\u30a4\u30eb\u3067\u3042\u308c\u3070xml\u3068\u3057\u3066\u8aad\u307f\u8fbc\u3080\u3002\n * \u7121\u3044\u5834\u5408\u306f\u3001\u6a19\u6e96\u5165\u529b\u3092\u8aad\u307f\u8fbc\u3080\n *\/\nif(! isset($argv[1])) die("\u5f15\u6570\u304c\u3042\u308a\u307e\u305b\u3093\\n");\n \n$images = glob(str_replace('.png', '.*.png', $argv[1]));\nif(count($images) === 0) die("\u753b\u50cf\u30d5\u30a1\u30a4\u30eb\u304c\u898b\u3064\u304b\u308a\u307e\u305b\u3093: {$argv[1]}\\n");\n?>\n<!DOCTYPE html>\n<html lang="ja">\n <head>\n <meta charset="UTF-8">\n <meta name="viewport" content="width=device-width, initial-scale=1.0">\n <title>BLAST\u7d50\u679c<\/title>\n <style>\n body { font-family: monospace; }\n .blast-image { max-width: 100%; height: auto; }\n <\/style>\n <\/head>\n <body>\n<?php\n foreach($images as $image){\n $gene = explode('.', basename($image, '.png'));\n $gene = array_pop($gene);\n?>\n <div>\n <h3>Gene: <?php echo htmlspecialchars($gene); ?><\/h3>\n <img src="<?php echo htmlspecialchars($image); ?>">\n <\/div>\n<?php\n }\n?>\n <\/body>\n<\/html>\n<\/pre>\n<\/div>\n\u6b21\u306e\u3088\u3046\u306b\u5b9f\u884c\u3059\u308b\u3002<\/p>\n
\n$ php scripts\/make_html.php tmp\/2p-7.png >2p-7.html\n<\/pre><\/div>\nDocker\u306e\u30b3\u30f3\u30c6\u30ca\u306b\u3059\u308b<\/h2>\n
\u5e83\u304f\u4e00\u822c\u306e\u5229\u7528\u8005\u306b\u4f7f\u3063\u3066\u3082\u3089\u3046\u305f\u3081\u306bDocker\u306e\u30a4\u30e1\u30fc\u30b8\u3092\u4f5c\u6210\u3059\u308b\u3002\nDocker\u306e\u30a4\u30e1\u30fc\u30b8\u3092\u3064\u304f\u308b\u3053\u3068\u306b\u3088\u3063\u3066\u3001blast\u306a\u3069\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3059\u308b\u5fc5\u8981\u304c\u306a\u304f\u306a\u308b\u3002<\/p>\n
\u624b\u9806\u3092\u4e00\u822c\u5316\u3059\u308b<\/h3>\n
\u56fa\u6709\u306e\u30d5\u30a1\u30a4\u30eb\u540d\u3092\u306a\u304f\u3057\u3066\u3001\u9023\u7d9a\u7684\u306b\u30d7\u30ed\u30b0\u30e9\u30e0\u304c\u5b9f\u884c\u3055\u308c\u308b\u3088\u3046\u306b make \u3068\u3044\u3046\u3057\u304f\u307f\u3092\u4f7f\u3046\u3002<\/p>\n
\u4eca\u56de\u884c\u3063\u305f\u306e\u306f\u4e0b\u8a18\u306e\u624b\u9806\u3067\u3001\u524d\u306e\u30d5\u30a1\u30a4\u30eb\u304b\u3089\u6b21\u306e\u30d5\u30a1\u30a4\u30eb\u3092\u3064\u304f\u308b\u3068\u3044\u3046\u3088\u3046\u306b\u306a\u3063\u3066\u3044\u308b\u3002\n\u3053\u306e\u4f9d\u5b58\u95a2\u4fc2\u3092Makefile\u306b\u66f8\u304d\u51fa\u3059\u3002<\/p>\n
\n- \u30ea\u30d5\u30a1\u30ec\u30f3\u30b9\u304b\u3089makeblastdb<\/li>\n
- fastq.gz\u304b\u3089fasta<\/li>\n
- fasta\u304b\u3089blast_xml<\/li>\n
- blast_xml\u304b\u3089aln<\/li>\n
- aln\u304b\u3089Robj (\u30ab\u30a6\u30f3\u30c8\u30c7\u30fc\u30bf)<\/li>\n
- Robj\u304b\u3089png<\/li>\n
- png\u304b\u3089index.html<\/li>\n<\/ul>\n
<\/p>\n
\n Makefile<\/h5>\n\nSHELL = \/bin\/bash\nWORK_DIR = tmp\nSCRIPT_DIR ?= scripts\/\n \n.SECONDARY:\n \nFASTQ = $(wildcard raw_fastq\/*.fastq.gz)\nHTML = $(patsubst raw_fastq\/%.fastq.gz, %.html, $(FASTQ))\nREF = $(WORK_DIR)\/reference\n \nall: $(HTML)\n \nclean:\n\trm -rf $(WORK_DIR) $(HTML) \n \ndownload-test:\n\t@mkdir -p $(dir $@)\n\tcurl -o $@ https:\/\/kiku3.tsbio.info\/~takamasa\/260917Honda\/ref\/SUDL.fa\n\tcurl -O https:\/\/kiku3.tsbio.info\/~takamasa\/260917Honda\/60-1380693045_FASTQ.zip\n\tunzip 60-1380693045_FASTQ.zip\n\trm 60-1380693045_FASTQ.zip\n \n%.html: $(SCRIPT_DIR)\/make_html.php $(WORK_DIR)\/%.png\n\tphp $^ >$@\n\t\n$(WORK_DIR)\/%.png: $(SCRIPT_DIR)\/pile.R $(WORK_DIR)\/%.Robj $(REF).fa\n\tRscript $^ $(basename $@) && touch $@\n \n$(WORK_DIR)\/%.Robj: $(SCRIPT_DIR)\/count_read.R $(WORK_DIR)\/%.aln\n\tRscript $^ $@\n \n$(WORK_DIR)\/%.aln: $(SCRIPT_DIR)\/parse_blastxml.php $(WORK_DIR)\/%.xml\n\tphp $^ >$@\n \n$(WORK_DIR)\/%.xml: $(WORK_DIR)\/%.fasta $(REF).nin\n\tblastn -query $< -db $(REF) -out $@ -outfmt 5 -max_target_seqs 1 -max_hsps 1\n \n$(WORK_DIR)\/%.fasta: raw_fastq\/%.fastq.gz\n\t@mkdir -p $(dir $@)\n\tzcat $< | sed -e "1~4s\/^@\/>\/;3~4d;4~4d" >$@\n \n$(REF).nin: $(REF).fa\n\tmakeblastdb -in $< -out $(REF) -dbtype nucl\n \n$(REF).fa: $(wildcard reference\/*.fa) $(wildcard reference\/*.fasta)\n\t@mkdir -p $(dir $@)\n\tcat $^ >$@\n \nDOCKER_USER = takamasa\nIMAGE_NAME = analyze-ez-pcr\nVERSION = 1.0\n \ndocker-build:\n\tdocker build \\\n\t\t-t ${DOCKER_USER}\/${IMAGE_NAME}:${VERSION} \\\n\t\t-t ${DOCKER_USER}\/${IMAGE_NAME}:latest .\n \ndocker-push:\n\tdocker push ${DOCKER_USER}\/${IMAGE_NAME}:${VERSION}\n\tdocker push ${DOCKER_USER}\/${IMAGE_NAME}:latest\n<\/pre>\n<\/div>\n\u3053\u3093\u306a\u611f\u3058\u3067\u5b9f\u884c\u3059\u308b\u3002<\/p>\n
\n$ make 2p-7.html\n<\/pre><\/div>\nDocker\u306e\u30a4\u30e1\u30fc\u30b8\u3092\u3064\u304f\u308b<\/h3>\n
Dockerfile\u3092\u3064\u304f\u308b\u3002\n\u3053\u308c\u306f\u65e2\u5b58\u306e\u30a4\u30e1\u30fc\u30b8\u304b\u3089\u30ab\u30b9\u30bf\u30de\u30a4\u30ba\u3057\u305f\u30a4\u30e1\u30fc\u30b8\u3092\u3064\u304f\u308b\u624b\u9806\u3092\u66f8\u3044\u305f\u3082\u306e\u3002<\/p>\n
\u4e00\u9023\u306e\u51e6\u7406\u3092\u884c\u3046\u306e\u306b\u5fc5\u8981\u306a\u30d1\u30c3\u30b1\u30fc\u30b8\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3001\u4f5c\u6210\u3057\u305f\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u30b3\u30d4\u30fc\u3059\u308b\u3002<\/p>\n
<\/p>\n
\n Dockerfile<\/h5>\n\nFROM ubuntu:22.04\n \n# \u74b0\u5883\u5909\u6570\u306e\u8a2d\u5b9a\uff08\u5bfe\u8a71\u578b\u30d7\u30ed\u30f3\u30d7\u30c8\u3092\u7121\u52b9\u5316\uff09\nENV DEBIAN_FRONTEND=noninteractive\n \n# \u5fc5\u9808\u30d1\u30c3\u30b1\u30fc\u30b8\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\nRUN apt-get update && apt-get install -y --no-install-recommends \\\n make curl gzip unzip \\\n ncbi-blast+ \\\n php-cli php-xml libxml2-dev \\\n r-base-core r-base-dev \\\n libcurl4-openssl-dev libssl-dev \\\n && rm -rf \/var\/lib\/apt\/lists\/*\n \n# R\u306e\u8ffd\u52a0\u30d1\u30c3\u30b1\u30fc\u30b8\u304c\u5fc5\u8981\u306a\u5834\u5408\u306f\u3053\u3053\u3067\u6307\u5b9a\uff08\u4f8b: ggplot2 \u3084 Bioconductor\u7b49\uff09\n# RUN Rscript -e "install.packages(c('ggplot2', 'dplyr'), repos='https:\/\/cloud.r-project.org\/')"\n \nWORKDIR \/app\nCOPY scripts\/ \/app\/scripts\/\nCOPY Makefile \/app\/Makefile\n \nENV SCRIPT_DIR=\/app\/scripts\n \n# \u4f5c\u696d\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u306e\u8a2d\u5b9a\nWORKDIR \/workspace\n \n# \u30b3\u30f3\u30c6\u30ca\u8d77\u52d5\u6642\u306b\u81ea\u52d5\u3067 make \u3092\u5b9f\u884c\u3059\u308b\u5834\u5408\u306e\u8a2d\u5b9a\nCMD ["make", "-f", "\/app\/Makefile"]\n<\/pre>\n<\/div>\n\u30a4\u30e1\u30fc\u30b8\u3092\u4f5c\u6210<\/p>\n
\n$ docker build -t mypipeline\n<\/pre><\/div>\n\u5b9f\u884c<\/p>\n
\n$ docker run --rm -v .:\/workspace mypipeline\n<\/pre><\/div>\n","protected":false},"excerpt":{"rendered":"\u76ee\u7684 \u5909\u7570\u682a\u306e\u30b9\u30af\u30ea\u30fc\u30cb\u30f3\u30b0\u3092\u884c\u3044\u3001\u3044\u304f\u3064\u304b\u5019\u88dc\u3092\u5f97\u308b\u3053\u3068\u304c\u3067\u304d\u307e\u3057\u305f\u3002 \u6b21\u306f\u539f\u56e0\u907a\u4f1d\u5b50\u306e\u540c\u5b9a\u306b\u9032\u307f\u305f\u3044\u306e\u3067\u3059\u304c\u3001\u65e2\u77e5\u306e\u907a\u4f1d\u5b50\u306e\u30a2\u30ea\u30eb\u304b\u3082\u3057\u308c\u307e\u305b\u3093\u3002 \u305d\u306e\u5834\u5408\u3001\u5019\u88dc\u907a\u4f1d\u5b50\u3092\u30b5\u30f3\u30ac\u30fc\u6cd5\u3067\u30b7\u30fc\u30af\u30a8\u30f3\u30b9\u3057\u3066\u3001\u65b0\u898f\u3067\u3042\u308b\u3053\u3068\u3092 […]","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-3471","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/pages\/3471","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/comments?post=3471"}],"version-history":[{"count":42,"href":"https:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/pages\/3471\/revisions"}],"predecessor-version":[{"id":3536,"href":"https:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/pages\/3471\/revisions\/3536"}],"wp:attachment":[{"href":"https:\/\/biochemistry.isc.chubu.ac.jp\/labo\/suzuki\/wp-json\/wp\/v2\/media?parent=3471"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}