{"id":198,"date":"2022-01-03T11:31:43","date_gmt":"2022-01-03T03:31:43","guid":{"rendered":"https:\/\/linguopeng.top\/?p=198"},"modified":"2022-01-03T11:31:45","modified_gmt":"2022-01-03T03:31:45","slug":"%e5%be%ae%e7%94%9f%e7%89%a9%e7%9a%84hgt%e9%a2%84%e6%b5%8b","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=198","title":{"rendered":"\u5fae\u751f\u7269\u7684HGT\u9884\u6d4b"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>\n#\u53c2\u8003https:\/\/github.com\/qiyunlab\/HGTector\/\n#Zhu Q, Kosoy M, Dittmar K. HGTector: an automated method facilitating genome-wide discovery of putative #horizontal gene transfers. BMC Genomics. 2014. 15:717.\n#\u7b80\u4e66https:\/\/www.jianshu.com\/p\/9c529c9064d8\n\n#\u4e0b\u8f7dnr\u6570\u636e\u5e93\nascp -v -k 1 -T -l 300m -i ~\/asperaweb_id_dsa.openssh anonftp@ftp.ncbi.nlm.nih.gov:\/blast\/db\/FASTA\/nr.gz .\/\n#\u4e0b\u8f7d\u5206\u7c7b\u4fe1\u606f\nascp -i ~\/asperaweb_id_dsa.openssh  -QTr -l500m  anonftp@ftp.ncbi.nlm.nih.gov:pub\/taxonomy\/taxdump.tar.gz .\/\n#\u4e0b\u8f7d\u5e8f\u5217\u4fe1\u606f\nascp -P33001 -l 500m --mode recv -i ~\/asperaweb_id_dsa.openssh  -QTr -l600m  anonftp@ftp-private.ncbi.nlm.nih.gov:pub\/taxonomy\/accession2taxid\/prot.accession2taxid.gz .\/\n#\u5b89\u88c5csvtk \uff0ctaxonkit \u5de5\u5177\nconda install csvtk -y\r\nconda install taxonkit -y\n#\u6784\u5efanr\u6570\u636e\u5e93\nnohup makeblastdb -parse_seqids -in nr.fa -dbtype prot -out nr &amp;\n#\u5206\u522b\u63d0\u53d6\u75c5\u6bd2\uff0c\u53e4\u7ec6\u83cc\uff0c\u7ec6\u83cc\uff0c\u771f\u83cc\u5e8f\u5217\u4fe1\u606f\n#ids 10239 virus \u75c5\u6bd2\r\n#ids 2157 Archaea \u53e4\u83cc\r\n#ids 2 Bacteria \u7ec6\u83cc\r\n#ids 4751 Fungi \u771f\u83cc\ntaxonkit list -j 45 --ids 10239 --indent \"\" --data-dir .\/taxdump\/ > Virus.list\r\ntaxonkit list -j 45 --ids 2157  --indent \"\" --data-dir .\/taxdump\/ > Archaea.list\r\ntaxonkit list -j 45 --ids 2 --indent \"\" --data-dir .\/taxdump\/ > Bacteria.list\r\ntaxonkit list -j 45 --ids 4751 --indent \"\" --data-dir .\/taxdump\/ > Fungi.list\n\nzcat prot.accession2taxid | csvtk -t grep -f taxid -P ..\/nr\/Virus.list | csvtk -t cut -f accession.version > Virus.taxid.acc.txt\r\nzcat prot.accession2taxid | csvtk -t grep -f taxid -P ..\/nr\/Archaea.list | csvtk -t cut -f accession.version > Archaea.taxid.acc.txt\r\nzcat prot.accession2taxid | csvtk -t grep -f taxid -P ..\/nr\/Bacteria.list | csvtk -t cut -f accession.version > Bacteria.taxid.acc.txt\r\nzcat prot.accession2taxid | csvtk -t grep -f taxid -P ..\/nr\/Fungi.list | csvtk -t cut -f accession.version > Fungi.taxid.acc.txt\n\nblastdb_aliastool -seqidlist Virus.taxid.acc.txt -db .\/nr\/nr -out nr_virues -title nr_virues\r\nblastdb_aliastool -seqidlist Archaea.taxid.acc.txt -db .\/nr\/nr -out nr_archaea -title nr_archaea\r\nblastdb_aliastool -seqidlist Bacteria.taxid.acc.txt -db .\/nr\/nr -out nr_bacteria -title nr_bacteria\r\nblastdb_aliastool -seqidlist Fungi.taxid.acc.txt -db .\/nr\/nr -out nr_fungi -title nr_fungi\n##########\n#blastdb_aliastool -seqidlist Virus.taxid.acc.txt -db .\/nr\/nr -out nr_virues -title nr_virues\r\n#Created protein BLAST (alias) database nr_virues with 898896 sequences\r\n#blastdb_aliastool -seqidlist Bacteria.taxid.acc.txt -db .\/nr\/nr -out nr_bacteria -title nr_bacteria\r\n#Created protein BLAST (alias) database nr_bacteria with 28850848 sequences\r\n#blastdb_aliastool -seqidlist Fungi.taxid.acc.txt -db .\/nr\/nr -out nr_fungi -title nr_fungi\r\n#Created protein BLAST (alias) database nr_fungi with 2684352 sequences\r\n#blastdb_aliastool -seqidlist Archaea.taxid.acc.txt -db .\/nr\/nr -out nr_archaea -title nr_archaea\r\n#Created protein BLAST (alias) database nr_archaea with 608013 sequences\r\n###################\nblastdbcmd -db nr_virues -entry all -dbtype prot -out nr_Virus.fa\r\nblastdbcmd -db nr_archaea -entry all -dbtype prot -out nr_Archaea.fa\r\nblastdbcmd -db nr_bacteria -entry all -dbtype prot -out nr_Bacteria.fa\r\nblastdbcmd -db nr_fungi -entry all -dbtype prot -out nr_Fungi.fa\n#\u5408\u5e76\u5fae\u751f\u7269\u5e8f\u5217\ncat nr_Virus.fa nr_Archaea.fa nr_Bacteria.fa nr_Fungi.fa >nr_B_F_A_V.fa\n#\u5e8f\u5217\u4e0e\u5206\u7c7b\u5408\u5e76\u6784\u5efa\u5fae\u751f\u7269\u6570\u636e\u5e93\ndiamond makedb --threads 45 --in nr_B_F_A_V.fa --taxonmap prot.accession2taxid --taxonnodes taxdump\/nodes.dmp --taxonnames taxdump\/names.dmp --db diamond\/nr_B_F_A_V\n#\u6fc0\u6d3bhgtector\u73af\u5883\uff0c\u8fdb\u884c\u5206\u6790 \nhgtector search -i FAHBZ9L5_CDS.faa -o search -m diamond -p 45 -d diamond\/nr_B_F_A_V -t taxdump\r\nhgtector analyze -i search -o analyze -t ..\/taxdump\n\n\n\n<\/code><\/pre>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-198","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/198","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=198"}],"version-history":[{"count":1,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/198\/revisions"}],"predecessor-version":[{"id":200,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/198\/revisions\/200"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=198"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=198"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=198"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}