{"id":532,"date":"2020-08-08T15:38:39","date_gmt":"2020-08-08T07:38:39","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=532"},"modified":"2020-08-24T10:18:19","modified_gmt":"2020-08-24T02:18:19","slug":"%e6%a0%b9%e6%8d%aegff%e6%96%87%e4%bb%b6%e7%bb%9f%e8%ae%a1exon%e3%80%81intron%e9%95%bf%e5%ba%a6%e5%88%86%e5%b8%83%e5%9b%be","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=532","title":{"rendered":"\u6839\u636egff\u6587\u4ef6\u7edf\u8ba1exon\u3001intron\u957f\u5ea6\u5206\u5e03\u56fe"},"content":{"rendered":"<p>\u4e0b\u8f7d\u9700\u8981\u7684\u811a\u672c\u548c\u5b89\u88c5Python\u6a21\u5757<\/p>\n<pre>wget https:\/\/github.com\/irusri\/Extract-intron-from-gff3\/archive\/master.zip\r\nunzip master.zip\r\nrm master.zip && cd Extract-intron-from-gff3-master\/scripts\/\r\nsudo chmod 755 *\r\npip install misopy\r\npip install gffutils<\/pre>\n<p>\u83b7\u53d6exon\u3001intron\u7684gff\u6587\u4ef6\u5e76\u63d0\u53d6DNA\u5e8f\u5217<\/p>\n<pre>python \/opt\/biosoft\/Extract-intron-from-gff3-master\/scripts\/extract_intron_gff3_from_gff3.py out.gff3 out_intron.gff3\r\n##\u7ed3\u679c\u6587\u4ef6out_intron.gff3_introns.gff3\r\nawk '\/intron\\t\/{print}' out_intron.gff3_introns.gff3 | sort -k 1,1 -k4,2n   > processed_intron.gff3\r\nawk '\/exon\\t\/{print}' out_intron.gff3_introns.gff3 | sort -k 1,1 -k4,2n   > processed_exon.gff3\r\nperl \/opt\/biosoft\/Extract-intron-from-gff3-master\/scripts\/extract_seq_from_gff3.pl -d out.tmp\/genome.fasta - processed_intron.gff3 > output_intron.fa\r\nperl \/opt\/biosoft\/Extract-intron-from-gff3-master\/scripts\/extract_seq_from_gff3.pl -d out.tmp\/genome.fasta - processed_exon.gff3 > output_exon.fa\r\n##\u5bf9\u5e8f\u5217\u91cd\u547d\u540d\r\ngenome_seq_clear.pl output_intron.fa --seq_prefix intron --min_length 1 --line_length -1 > output_intron_rename.fa\r\ngenome_seq_clear.pl output_exon.fa --seq_prefix exon --min_length 1 --line_length -1 > output_exon_rename.fa\r\n##\u83b7\u5f97\u6bcf\u6761\u5e8f\u5217\u7684\u957f\u5ea6\u4fe1\u606f\r\nsamtools faidx output_intron_rename.fa\r\ncut -f 1,2 output_intron_rename.fa.fai > output_intron_length.txt\r\nsamtools faidx output_exon_rename.fa\r\ncut -f 1,2 output_exon_rename.fa.fai > output_exon_length.txt\r\n##R\u753b\u56fe\r\nlibrary(ggplot2)\r\nlibrary(patchwork)\r\ndata <- read.table(\"output_gene_length.txt\",header=T,check.names=F)\r\np1 <- ggplot(data,aes(length))+ geom_line(stat=\"density\",color=\"red\")+theme_classic()+theme(axis.title = element_text(size=24),axis.text = element_text(size = 22,color = \"black\"))\r\np1\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>\u4e0b\u8f7d\u9700\u8981\u7684\u811a\u672c\u548c\u5b89\u88c5Python\u6a21\u5757 wget https:\/\/github.com\/irusri\/Extract-intron-from-gff3\/archive\/master.zip unzip master.zip rm master.zip &#038;&#038; cd Extract-intron-from-gff3-master\/scripts\/ sudo chmod 755 * pip install misopy pip install gffutils \u83b7\u53d6exon\u3001intron\u7684gff\u6587\u4ef6\u5e76\u63d0\u53d6DNA\u5e8f\u5217 python \/opt\/biosoft\/Extract-intron-from-gff3-master\/scripts\/extract_intron_gff3_from_gff3.py out.gff3 out_intron.gff3 ##\u7ed3\u679c\u6587\u4ef6out_intron.gff3_introns.gff3 awk &#8216;\/intron\\t\/{print}&#8217; out_intron.gff3_introns.gff3 | sort -k 1,1 -k4,2n > processed_intron.gff3 awk &#8216;\/exon\\t\/{print}&#8217; out_intron.gff3_introns.gff3 | sort -k 1,1 -k4,2n > processed_exon.gff3 perl \/opt\/biosoft\/Extract-intron-from-gff3-master\/scripts\/extract_seq_from_gff3.pl -d out.tmp\/genome.fasta &#8211; processed_intron.gff3 > output_intron.fa perl [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/532"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=532"}],"version-history":[{"count":5,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/532\/revisions"}],"predecessor-version":[{"id":557,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/532\/revisions\/557"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=532"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=532"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=532"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}