{"id":80,"date":"2012-08-22T19:35:58","date_gmt":"2012-08-22T11:35:58","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=80"},"modified":"2013-11-04T18:34:03","modified_gmt":"2013-11-04T10:34:03","slug":"blast2go%e6%9c%ac%e5%9c%b0%e6%95%b0%e6%8d%ae%e5%ba%93%e5%ae%89%e8%a3%85","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=80","title":{"rendered":"blast2go\u672c\u5730\u6570\u636e\u5e93\u5b89\u88c5\u548c\u4f7f\u7528"},"content":{"rendered":"

1. Download all necessary files<\/h1>\n
\r\n$ wget -c -b -N --progress=dot:mega http:\/\/archive.geneontology.org\/latest-full\/go_201310-assocdb-data.gz\r\n$ wget -c -b -N --progress=dot:mega ftp:\/\/ftp.ncbi.nlm.nih.gov\/gene\/DATA\/gene_info.gz\r\n$ wget -c -b -N --progress=dot:mega ftp:\/\/ftp.ncbi.nlm.nih.gov\/gene\/DATA\/gene2accession.gz   \r\n$ wget -c -b -N --progress=dot:mega ftp:\/\/ftp.pir.georgetown.edu\/databases\/idmapping\/idmapping.tb.gz\r\n$ wget -c -b -N --progress=dot:mega http:\/\/blast2go.com\/data\/blast2go\/b2g4pipe_v2.5.zip\r\n$ wget -c -b -N --progress=dot:mega http:\/\/blast2go.com\/public-data\/local_b2g_db.zip\r\n<\/pre>\n
2. Unzip all\u00a0 files<\/h1>\n
\r\n$ gzip -dv go_201207-assocdb-data.gz\r\n$ gzip -dv gene_info.gz\r\n$ gzip -dv gene2accession.gz\r\n$ gzip -dv idmapping.tb.gz\r\n$ unzip b2g4pipe_v2.5.zip\r\n$ unzip local_b2g_db.zip\r\n$ cp  local_b2g_db\/* .\r\n<\/pre>\n
4. Execute the file b2gdb.sql to create a database (default name: b2gdb), additional tables and a public user for restricted access (select only).<\/h1>\n
\u65b0\u5efa\u6587\u4ef6install_blast2goDB.sh,\u5185\u5bb9\u5982\u4e0b\uff1a<\/p>\n
\r\n#!\/bin\/sh\r\ngodbname=go_201310-assocdb-data\r\ndbname=b2g\r\ndbuser=root\r\ndbpass=passwd \u00a0\u00a0\u00a0 #\u8fd9\u4e2a\u8981\u4fee\u6539\r\ndbhost=127.0.0.1\r\npath=$PWD         #\u6570\u636e\u6587\u4ef6\u7684\u5b58\u653e\u8def\u5f84\r\n\r\nmysql -h$dbhost -P 3306 -u$dbuser -p$dbpass $dbname < b2gdb.sql \r\n\r\nmysql -h$dbhost -u$dbuser -p$dbpass $dbname < $godbname\r\nmysql -h$dbhost -u$dbuser -p$dbpass $dbname -e\"LOAD DATA LOCAL INFILE '$path\"\/gene2accession\"' INTO TABLE gene2accession FIELDS TERMINATED BY '\\t' LINES TERMINATED BY '\\n';\"\r\nmysql -h$dbhost -u$dbuser -p$dbpass $dbname -e\"LOAD DATA LOCAL INFILE '$path\"\/gene_info\"' INTO TABLE gene_info FIELDS TERMINATED BY '\\t' LINES TERMINATED BY '\\n';\"\r\n\r\necho Finished, now use Blast2GO to import the PIR mapping data-file;\r\n<\/pre>\n
\u4f7finstall_blast2goDB.sh\u53ef\u6267\u884c\uff0c\u5e76\u8fd0\u884c\u8be5\u811a\u672c\u3002\u8fd9\u4e00\u6b65\u662f\u5c06 go_201207-assocdb-data.gz\uff0cgene2accession \u548c gene_info \u5bfc\u5165\u5230 b2gdb \u6570\u636e\u5e93\u4e2d.<\/p>\n
5. Import the last mapping file from PIR<\/h1>\n
\u65b0\u7248\u672c\u4e2d\u662f\u8fd9\u6837\u8fd0\u884c\u7684\uff1a<\/p>\n
\r\njava -cp .:mysql-connector-java-5.0.8-bin.jar: ImportIdMapping \\\r\nidmapping.tb localhost b2gdb blast2go blast4it\r\n<\/pre>\n
\u65b0\u7248\u672c\u4e2dlocal_b2g_db.zip\u4e2d\u67093\u4e2a\u6587\u4ef6\uff1ab2gdb.sql\uff0cImportIdMapping.class\u548cmysql-connector-java-5.0.8-bin.jar\u3002\u901a\u8fc7b2gdb.sql\u6587\u4ef6\u6765\u521b\u5efamysql\u6570\u636e\u5e93\u548c\u8868\u3002\u901a\u8fc7\u8be5\u6587\u4ef6\uff0c\u5176\u521b\u5efa\u4e86\u6570\u636e\u5e93b2gdb,\u5e76\u521b\u5efa\u4e86\u5bf9b2gdb\u6570\u636e\u5e93\u62e5\u6709\u6700\u5927\u6743\u9650\u7684mysql\u7528\u6237blas2go,\u5bc6\u7801blast4it\u3002\u540c\u65f6\u8fd0\u884c\u4e0a\u8ff0\u547d\u4ee4\u9700\u8981\u540c\u65f6\u6709ImportIdMapping.class\u548cmysql-connector-java-5.0.8-bin.jar\u8fd9\u4e24\u4e2a\u6587\u4ef6\u3002
\n\u8fd9\u4e00\u6b65\u662f\u5c06 idmapping.tb \u5bfc\u5165\u5230\u672c\u5730 b2gdb \u6570\u636e\u5e93\u7684 gi2uniprot \u8868\u4e2d\u3002<\/p>\n
\u8001\u7248\u672c\u4e2d\u662f\u8fd9\u6837\u8fd0\u884c\u7684\uff1a<\/p>\n
\/home\/chenlianfu\/programs\/jre1.7.0_04\/bin\/java -cp \/home\/chenlianfu\/programs\/blast2go\/b2g4pipe\/blast2go.jar:\/home\/chenlianfu\/programs\/blast2go\/b2g4pipe\/ext\/mysql-connector-java-3.0.11-stabes-bin.jar es.blast2go.prog.util.ImportPIR idmapping.tb localhost b2g root passwd TRUE<\/pre>\n
\u8001\u7248\u672c\u4e2d\u4e00\u5b9a\u8981\u6ce8\u610f\uff0c\u547d\u4ee4\u8981\u9760\u81ea\u5df1\u7528\u624b\u4eb2\u81ea\u6572\u6253\u51fa\u6765\uff0c\u5982\u679c\u590d\u5236\u7684\u8bdd\uff0c\u4e00\u822c\u4f1a\u51fa\u73b0\u5982\u4e0b\u9519\u8bef<\/p>\n
Problem connecting to database b2g on localhost as root with password starts with *********: com.mysql.jdbc.Driver<\/pre>\n
\u800c\u5bfc\u5165\u6b63\u5e38\u4f1a\u63d0\u793a\u4e3a<\/p>\n
Open database connection to database b2g on 127.0.0.1 as root with password starts with *********\r\nOpen database connection to database b2g on 127.0.0.1 as root with password starts with *********<\/pre>\n
\u590d\u5236\u51fa\u7684\u8bed\u53e5\u548c\u624b\u5de5\u6572\u6253\u51fa\u7684\u8bed\u53e5\u8868\u9762\u770b\u4e0a\u53bb\u4e00\u6a21\u4e00\u6837\uff0c\u53ef\u80fd\u67d0\u4e2a\u7b26\u53f7\u5176\u5b9e\u4e0d\u4e00\u81f4\uff0c\u673a\u5668\u8bc6\u522b\u4e0d\u51fa\u6765\u3002\u8fd9\u70b9\u5343\u4e07\u8981\u6ce8\u610f\uff0c\u4e0d\u7136\u7b2c 5 \u6b65\u6b7b\u6d3b\u4e5f\u8fc7\u4e0d\u53bb\u4e86\u3002<\/p>\n
\u53ef\u4ee5\u901a\u8fc7\u5c06 mysql \u8bed\u53e5\u6765\u67e5\u8be2\u5bfc\u5165\u4e86\u591a\u5c11\u884c\u6570\u636e\u5230\u8868\u4e2d\uff1a<\/p>\n
mysql> SELECT COUNT(*) FROM gi2uniprot;\r\n+----------+\r\n| COUNT(*) |\r\n+----------+\r\n| 40344363 |\r\n+----------+\r\n1 row in set (0.00 sec)<\/pre>\n
6. \u8fd0\u884cblast2go<\/h1>\n
1. \u56fe\u5f62\u5316\u8fd0\u884c<\/h2>\n
  \u8fd0\u884c\u51fa\u73b0\u4e86\u89e3\u51b3\u4e0d\u4e86\u7684\u95ee\u9898\uff0c\u53ef\u4ee5\u5c1d\u8bd5\u5207\u6362\u4e00\u4e2a\u5168\u65b0\u7684\u7528\u6237\u53bb\u8fd0\u884cblast2go\u3002
\n  \u4f7f\u7528b2g4pipe\u8fdb\u884c\u4e0d\u7528\u8054\u7f51\u7684\u8fd0\u884c\uff1a<\/p>\n
\r\n$ java -Xmx1000m -cp *:ext\/*: es.blast2go.Blast2GO\r\n<\/pre>\n
  \u4e0d\u4f7f\u7528b2g4pipe\u8fdb\u884c\u8054\u7f51\u7684\u8fd0\u884c\uff1a<\/p>\n
\r\n\u66fe\u7ecf\uff1a\r\n$ javaws http:\/\/www.blast2go.com\/webstart\/makeJnlp.php?mem=1000\r\n\u73b0\u5728\uff1a\r\n$ javaws http:\/\/www.blast2go.com\/webstart\/blast2go1000.jnlp\r\n<\/pre>\n
2. \u547d\u4ee4\u884c\u8fd0\u884c<\/h2>\n
  \u547d\u4ee4\u884c\u8fd0\u884c\u4f7f\u7528\u4e86b2g4pipe, \u5148\u4fee\u6539b2gPipe.properties\u4e2d\u7684\u6570\u636e\u5e93\u53c2\u6570\uff0c\u518d\u8fd0\u884c\u3002\u9700\u8981\u5148\u83b7\u5f97blast\u548cinterproscan\u7684\u6ce8\u91ca\u7ed3\u679c\uff0c\u518d\u8fdb\u884c\u547d\u4ee4\u884c\u8fd0\u884c\u3002\u6709\u4e24\u79cd\u8fd0\u884c\u7684\u65b9\u6cd5\uff1a<\/p>\n
\r\n$ java -Xmx1000m -cp *:ext\/*: es.blast2go.prog.B2GAnnotPipe\r\n$ java -Xmx1000m -jar blast2go.jar\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
1. Download all necessary files $ wget – … \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[3],"tags":[16],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/80"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=80"}],"version-history":[{"count":13,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/80\/revisions"}],"predecessor-version":[{"id":2003,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/80\/revisions\/2003"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=80"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=80"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=80"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}