{"id":767,"date":"2024-09-12T16:31:43","date_gmt":"2024-09-12T08:31:43","guid":{"rendered":"https:\/\/linguopeng.top\/?p=767"},"modified":"2024-09-12T17:00:13","modified_gmt":"2024-09-12T09:00:13","slug":"%e6%af%94%e5%af%b9","status":"publish","type":"post","link":"https:\/\/linguopeng.top\/?p=767","title":{"rendered":"\u6bd4\u5bf9"},"content":{"rendered":"\n<pre class=\"wp-block-code\"><code>#\u4fee\u6539\u86cb\u767d\u6587\u4ef6\u540d\n# singularity exec orthomcl_latest.sif orthomclAdjustFasta \u6587\u4ef6\u540d \u6587\u4ef6\u8def\u5f84 1 \n# BLAST:\n# makeblastdb -in 12.fasta -dbtype prot\/nucl -out database\n# blastn -query FldC.fasta -out result.txt -db database -outfmt 6 -evalue 1e-5  -max_target_seqs 1 \n#find .\/ -name \"*.cds\" -print0 | xargs -0 -I {} cp {} .\/\n# blast result:\n#'query',\"subject\",\"identity\",\"Match_length\",\"Mismatch_length\",\"gap\",\"query_start\",\"query_end#\",\"subject_start\",\"subject_end\",\"e-vaule\",\"bitscore\"\n#singularity exec blast.sif blastn -query all.search.fasta -out result.txt -db target.fasta -outfmt 6 -evalue 1e-5  -max_target_seqs 1\n######################################strain_CagA############\nstrain_CagA&lt;-read.table(\"result.txt\",header = F)\nlibrary(tidyverse)\ncolnames(strain_CagA) &lt;- c('query',\"subject\",\"identity\",\"Match_length\",\n                           \"Mismatch_length\",\"gap\",\"query_start\",\"query_end\",\"subject_start\",\n                           \"subject_end\",\"e-vaule\",\"bitscore\")\nstrain_CagA&lt;-arrange(strain_CagA,desc(identity)) %>% as_tibble() %>%  filter(identity > 40 &amp; Match_length >70 ) \nstrain_CagA_count&lt;-filter(strain_CagA, subject == \"CagA26695\")\nstrain_CagA_unique&lt;-separate(data=strain_CagA_count, col=query, into=c(\"a\",\"b\",\"c\",\"d\"), sep = \"_\")\nstrain_CagA_unique&lt;-filter(strain_CagA_unique, d == \"&#91;CagA-F]\")\ndim(strain_CagA_unique)\nwrite_csv(strain_CagA_unique,\"strain_CagA_unique.csv\")\n######################################strain_HopQ############\nstrain_HopQ&lt;-read.table(\"result.txt\",header = F)\nlibrary(tidyverse)\ncolnames(strain_HopQ) &lt;- c('query',\"subject\",\"identity\",\"Match_length\",\n                           \"Mismatch_length\",\"gap\",\"query_start\",\"query_end\",\"subject_start\",\n                           \"subject_end\",\"e-vaule\",\"bitscore\")\nstrain_HopQ&lt;-arrange(strain_HopQ,desc(identity)) %>% as_tibble() %>%  filter(identity > 40 &amp; Match_length >70 ) \nstrain_HopQ_count&lt;-filter(strain_HopQ, subject == \"HopQ26695\")\nstrain_HopQ_unique&lt;-separate(data=strain_HopQ_count, col=query, into=c(\"a\",\"b\",\"c\",\"d\"), sep = \"_\")\nstrain_HopQ_unique&lt;-filter(strain_HopQ_unique, d == \"&#91;HopQ-F]\")\ndim(strain_HopQ_unique)\nwrite_csv(strain_HopQ_unique,\"strain_HopQ_unique.csv\")\n######################################strain_HtrA############\nstrain_HtrA&lt;-read.table(\"result.txt\",header = F)\nlibrary(tidyverse)\ncolnames(strain_HtrA) &lt;- c('query',\"subject\",\"identity\",\"Match_length\",\n                           \"Mismatch_length\",\"gap\",\"query_start\",\"query_end\",\"subject_start\",\n                           \"subject_end\",\"e-vaule\",\"bitscore\")\nstrain_HtrA&lt;-arrange(strain_HtrA,desc(identity)) %>% as_tibble() %>%  filter(identity > 40 &amp; Match_length >70 ) \nstrain_HtrA_count&lt;-filter(strain_HtrA, subject == \"HtrA26695\")\nstrain_HtrA_unique&lt;-separate(data=strain_HtrA_count, col=query, into=c(\"a\",\"b\",\"c\",\"d\"), sep = \"_\")\nstrain_HtrA_unique&lt;-filter(strain_HtrA_unique, d == \"&#91;HtrA-F]\")\ndim(strain_HtrA_unique)\nwrite_csv(strain_HtrA_unique,\"strain_HtrA_unique.csv\")\n######################################strain_IceA############\nstrain_IceA&lt;-read.table(\"result.txt\",header = F)\nlibrary(tidyverse)\ncolnames(strain_IceA) &lt;- c('query',\"subject\",\"identity\",\"Match_length\",\n                           \"Mismatch_length\",\"gap\",\"query_start\",\"query_end\",\"subject_start\",\n                           \"subject_end\",\"e-vaule\",\"bitscore\")\nstrain_IceA&lt;-arrange(strain_IceA,desc(identity)) %>% as_tibble() %>%  filter(identity > 40 &amp; Match_length >70 ) \nstrain_IceA_count&lt;-filter(strain_IceA, subject == \"IceA26695\")\nstrain_IceA_unique&lt;-separate(data=strain_IceA_count, col=query, into=c(\"a\",\"b\",\"c\",\"d\"), sep = \"_\")\nstrain_IceA_unique&lt;-filter(strain_IceA_unique, d == \"&#91;IceA-F]\")\ndim(strain_IceA_unique)\nwrite_csv(strain_IceA_unique,\"strain_IceA_unique.csv\")\n######################################strain_NapA############\nstrain_NapA&lt;-read.table(\"result.txt\",header = F)\nlibrary(tidyverse)\ncolnames(strain_NapA) &lt;- c('query',\"subject\",\"identity\",\"Match_length\",\n                           \"Mismatch_length\",\"gap\",\"query_start\",\"query_end\",\"subject_start\",\n                           \"subject_end\",\"e-vaule\",\"bitscore\")\nstrain_NapA&lt;-arrange(strain_NapA,desc(identity)) %>% as_tibble() %>%  filter(identity > 40 &amp; Match_length >70 ) \nstrain_NapA_count&lt;-filter(strain_NapA, subject == \"NapA26695\")\nstrain_NapA_unique&lt;-separate(data=strain_NapA_count, col=query, into=c(\"a\",\"b\",\"c\",\"d\"), sep = \"_\")\nstrain_NapA_unique&lt;-filter(strain_NapA_unique, d == \"&#91;NapA-F]\")\ndim(strain_NapA_unique)\nwrite_csv(strain_NapA_unique,\"strain_NapA_unique.csv\")\n######################################strain_OipA############\nstrain_OipA&lt;-read.table(\"result.txt\",header = F)\nlibrary(tidyverse)\ncolnames(strain_OipA) &lt;- c('query',\"subject\",\"identity\",\"Match_length\",\n                           \"Mismatch_length\",\"gap\",\"query_start\",\"query_end\",\"subject_start\",\n                           \"subject_end\",\"e-vaule\",\"bitscore\")\nstrain_OipA&lt;-arrange(strain_OipA,desc(identity)) %>% as_tibble() %>%  filter(identity > 40 &amp; Match_length >70 ) \nstrain_OipA_count&lt;-filter(strain_OipA, subject == \"OipA26695\")\nstrain_OipA_unique&lt;-separate(data=strain_OipA_count, col=query, into=c(\"a\",\"b\",\"c\",\"d\"), sep = \"_\")\nstrain_OipA_unique&lt;-filter(strain_OipA_unique, d == \"&#91;OipA-F]\")\ndim(strain_OipA_unique)\nwrite_csv(strain_OipA_unique,\"strain_OipA_unique.csv\")\n######################################strain_Saba############\nstrain_Saba&lt;-read.table(\"result.txt\",header = F)\nlibrary(tidyverse)\ncolnames(strain_Saba) &lt;- c('query',\"subject\",\"identity\",\"Match_length\",\n                           \"Mismatch_length\",\"gap\",\"query_start\",\"query_end\",\"subject_start\",\n                           \"subject_end\",\"e-vaule\",\"bitscore\")\nstrain_Saba&lt;-arrange(strain_Saba,desc(identity)) %>% as_tibble() %>%  filter(identity > 40 &amp; Match_length >70 ) \nstrain_Saba_count&lt;-filter(strain_Saba, subject == \"Saba26695\")\nstrain_Saba_unique&lt;-separate(data=strain_Saba_count, col=query, into=c(\"a\",\"b\",\"c\",\"d\"), sep = \"_\")\nstrain_Saba_unique&lt;-filter(strain_Saba_unique, d == \"Saba-F\")\ndim(strain_Saba_unique)\nwrite_csv(strain_Saba_unique,\"strain_Saba_unique.csv\")\n######################################strain_VacA############\nstrain_VacA&lt;-read.table(\"result.txt\",header = F)\nlibrary(tidyverse)\ncolnames(strain_VacA) &lt;- c('query',\"subject\",\"identity\",\"Match_length\",\n                           \"Mismatch_length\",\"gap\",\"query_start\",\"query_end\",\"subject_start\",\n                           \"subject_end\",\"e-vaule\",\"bitscore\")\nstrain_VacA&lt;-arrange(strain_VacA,desc(identity)) %>% as_tibble() %>%  filter(identity > 40 &amp; Match_length >70 ) \nstrain_VacA_count&lt;-filter(strain_VacA, subject == \"VacA26695\")\nstrain_VacA_unique&lt;-separate(data=strain_VacA_count, col=query, into=c(\"a\",\"b\",\"c\",\"d\"), sep = \"_\")\nstrain_VacA_unique&lt;-filter(strain_VacA_unique, d == \"&#91;VacA-F]\")\ndim(strain_VacA_unique)\nwrite_csv(strain_VacA_unique,\"strain_VacA_unique.csv\")\n######\nlibrary(openxlsx)\n# Write the dataframes to different sheets in the same Excel file\nwrite.xlsx(list(\"CagA\" = strain_CagA_unique, \"HopQ\" = strain_HopQ_unique,\n                \"HtrA\" = strain_HtrA_unique, \"IceA\" = strain_IceA_unique, \n                \"NapA\" = strain_NapA_unique, \"OipA\" = strain_OipA_unique, \n                \"Saba\" = strain_Saba_unique, \"VacA\" = strain_VacA_unique),\n           file = \"sample_26695_F.xlsx\")\n<\/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-767","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/767","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=767"}],"version-history":[{"count":4,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/767\/revisions"}],"predecessor-version":[{"id":773,"href":"https:\/\/linguopeng.top\/index.php?rest_route=\/wp\/v2\/posts\/767\/revisions\/773"}],"wp:attachment":[{"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=767"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=767"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/linguopeng.top\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=767"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}