{"id":746,"date":"2024-07-06T21:13:11","date_gmt":"2024-07-06T13:13:11","guid":{"rendered":"https:\/\/linguopeng.top\/?p=746"},"modified":"2024-07-06T21:46:06","modified_gmt":"2024-07-06T13:46:06","slug":"746","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=746","title":{"rendered":"\u6bd4\u8f83\u57fa\u56e0"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>#\u627e\u6587\u4ef6\nfind .\/ -name \"*.faa\" -print0 | xargs -0 -I {} cp {} .\/\n#\u6539\u540d\u79f0\u4e0e\u683c\u5f0f\u5316\nls *.faa|awk -F \"_\" '{print$1}' >junzhunname.txt\nls *.faa >id2\npaste junzhunname.txt id2 >idok\ncat idok |while read a b\ndo\necho \"orthomclAdjustFasta ${a} .\/${b} 1 \"\ndone |bash \nmkdir fasta\nmv *.fasta .\/fasta\ncd .\/fasta\nls *.fasta |awk -F \".\" '{print$1}' >name\ncat name |while read a \ndo\necho \"mv ${a}.fasta ${a}.faa\"\ndone |bash \n#\u63d0\u53d6\u5355\u62f7\u8d1d\u57fa\u56e0\u7c07\u7684\u5e8f\u5217\u4e3a\u6240\u6709\u83cc\u682a\u5171\u6709\u7684\u5e8f\u5217\nls *.fa >name\ncat *.fa >all.faa\ncat name |while read a\ndo\necho \"cat ${a} |head -n1 \"\ndone |bash >id.txt\nsed 's\/>\/\/g' id.txt >id2.txt\ncat all.faa |seqkit grep -f id2.txt >new.fa\n#\u67e5\u8be2\u76ee\u7684\u83cc\u682a\u662f\u5426\u542b\u6709\u76ee\u7684\u57fa\u56e0\nmakeblastdb -in target.fasta -dbtype prot\/nucl -out database\nblastn -query query.fasta -out ncbi120_ABC_out.txt -db database -outfmt 6 -evalue 1e-5  -max_target_seqs 1\n#\u5bf9\u4e0a\u8ff0\u57fa\u56e0\u8fdb\u884c\u7edf\u8ba1\n###########.carbohydrate ncbi120_ABC transporter permease#########\nstrain_ABC&lt;-read.table(\"ncbi120_ABC_out.txt\",header = F)\nlibrary(tidyverse)\nstrain_ABC&lt;-separate(data=strain_ABC, col=V1, into=c(\"strain\",\"gene\"), sep = \"_\")\ncolnames(strain_ABC) &lt;- c('strain', 'query',\"subject\",\"identity\",\"Match_length\",\n                              \"Mismatch_length\",\"gap\",\"query_start\",\"query_end\",\"subject_start\",\n                              \"subject_end\",\"e-vaule\",\"bitscore\")\nstrain_ABC&lt;-arrange(strain_ABC,desc(identity)) %>% as_tibble() %>%  filter(identity > 40 &amp; Match_length >70 ) \nstrain_ABC&lt;-strain_ABC&#91;!duplicated(strain_ABC$query),] \nstrain_ABC_count = as.data.frame(table(strain_ABC$strain))\ncolnames(strain_ABC_count)&lt;-c('strain',\"count\")\nstrain_ABC_count&lt;-arrange(strain_ABC_count,desc(count)) %>% as_tibble() \nstrain_ABC_count_12&lt;-filter(strain_ABC_count, strain == \"FNXHL2M3\" | strain == \"FJSNT37M5\"\n                            | strain == \"A14\" | strain == \"FFJND7M3\"\n                            | strain == \"FHuNMY10M3\" | strain == \"FSHXXA2M9\"\n                            | strain == \"FFJND17M1\" | strain == \"FFJNDD6M2\"\n                            | strain == \"FQHXN83M4\" | strain == \"FAHBZ9L5\"\n                            | strain == \"FGSYC12M4\" | strain == \"FHNXY15M2\")<\/code><\/pre>\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-746","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/746","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=746"}],"version-history":[{"count":3,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/746\/revisions"}],"predecessor-version":[{"id":749,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/746\/revisions\/749"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=746"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=746"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=746"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}