gtf_to_fasta transcripts.gtf genome.fa out_file 从GTF中提取转录本信息 利用AWK命令: sed 's/"/\t/g' mm10.gtf | awk -F '[\t|;]' '{ OFS="\t" } $3 == "transcript" {print $1,$4,$5,$10,0,$7} ' |sed 's/ transcript_id "//g'|sed 's/"//g'|less -S >mm10.transc...
The file UCSC_exons_modif.bed: chr1 11873 12227 uc001aaa.3 0 + chr1 12612 12721 uc001aaa.3 1 + chr1 13220 14409 uc001aaa.3 2 + chr1 11873 12227 uc010nxr.1 0 + chr1 12645 12697 uc010nxr.1 1 + chr1 13220 14409 uc010nxr.1 2 + chr1 11873 12227 uc010nxq.1 0 + chr1 ...
BedTool对象的创建可以使用interval file (BED, GFF, GTF, VCF, SAM, or BAM format)。 由文件创建BedTool对象: # 其中'test.bed' 是文件路径。test = pybedtools.BedTool('test.bed') 此外,也可以从字符串里创建: s='''chrX 1 100chrX 25 800'''## 由参数from_string控制a= pybedtools.BedTool(...
maskfasta Use intervals to mask sequences from aFASTAfile.nuc Profile the nucleotide contentofintervalsinaFASTAfile.[BAMfocused tools]multicov Counts coverage from multiple BAMs at specific intervals.tag TagBAMalignments based on overlapswithinterval files.[Statistical relationships]jaccard Calculate the Jacc...
Error: package or namespace load failed for ‘BED’: .onLoad failed in loadNamespace() for 'BED', details: call: connections[[connection]][["cache"]] error: subscript out of bounds … remove the BED folder located here:file.exists(file.path(Sys.getenv("HOME"), "R", "BED"))...
"-1 the input bed file is 1-based\n" "-h show this message\n" ); return1; } intmergeBed(intargc,char* argv[]) { inthelp =0; intn, i; char*out =0; intadd1 =0, add2 =0; while((n =getopt(argc, argv,"o:hr:l:1")) >=0) ...
PATRICE DOUGANFACTFILE
我对unix和linux脚本比较陌生,有几个问题:首先是我的剧本: for fileref in Ref/*.bed; do for filename in Data/*.bed; do bedops -e 1 $fileref $filename > "${fileref}${filename}.out" done done 我希望以两个文件(这两个文件是从循环遍历每个目录中收集的)作为输入来执行-e命令,并将输出文...
Perhaps you can work with the solution used in the attached file. It works with MAX and MIN to allow for start and end dates carrying over month-ends. and
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