找到约 15 条结果

问题 老师您好，我在运行megahit对200多个环境微生物宏基因组数据进行组装时，megahit报错Exit code -9

...O  sorting/seq_to_sdbg.cpp       :  191 - Read 65536 reads to search for mercy k-mers' 2025-05-26 08:15:16 - b'INFO  sorting/seq_to_sdbg.cpp       :  191 - Read 65536 reads to search for mercy k-mers' 2025-05-26 08:27:54 - Error occurs, please refer to /data2/temp/megahit/log for detai...

文章 借助perl脚本进行文件整理 | 将按第一列信息整理的文件改成按照第二列信息整理

...d_list> <out_file>\n" and die unless(@ARGV==2);open IN,"$ARGV[0]" or die "$!; can't open file $ARGV[0]\n";open OUT,">$ARGV[1]" or die "$!; can't open file $ARGV[1]\n";my%id;my%hash;while(<IN>){        chomp;        my@a=split(/\s/);        my@b=split(/;/,$a[1]);     ...

文章 Rocky 9下Rstudio-service配置教程

...udio/rserver.conf#设置内容如下：# Server Configuration Filersession-which-r=/share/biosoft/R/latest/bin/R 启动R 服务： rstudio-server start #启动RStudiorstudio-server status #查看RStudio状态 sudo systemctl status rstudio-server.service #查看状态 sudo systemctl start rstu...

文章 在使用miRDeep进行miRNA预测的时候报错

...体序列； perl miRDeep2.pl Total_reads_collapsed.fa GCA_000334115.1_Rhisol_AG1IA_1.0_genomic.fa Total_reads_collapsed_vs_genome.arf none -d  -g 100000 -l 500  -m 11 -v -P -n d 报错： The debug file is called error.output.mrd_04_09_2023_t_17_09_26 查看 error.output.mrd_04_09_2023_t_17...

问题 老师您好，我在运行megahit对200多个环境微生物宏基因组数据进行组装时，megahit报错Exit code -9

...O  sorting/seq_to_sdbg.cpp       :  191 - Read 65536 reads to search for mercy k-mers' 2025-05-26 08:15:16 - b'INFO  sorting/seq_to_sdbg.cpp       :  191 - Read 65536 reads to search for mercy k-mers' 2025-05-26 08:27:54 - Error occurs, please refer to /data2/temp/megahit/log for detai...

文章 利用biopython将cds序列翻译成蛋白序列

...th.abspath(args.out_dir)output_handle = open(dout+'/'+args.name+'.fa', "w")for rec in SeqIO.parse(args.fasta, "fasta"):    rec.seq=rec.seq.translate(table=args.table)    SeqIO.write(rec, output_handle, "fasta")output_handle.close()

问题 利用gff文件提取基因结构，结果文件是空的

...(/^#/);my @a = split /\t/, $_;next if $a[2]=~/exon/i;if ($a[2] =~/^mRNA$/i or $a[2] =~/^transcript$/i ) {($id1) =  ($a[8] =~ m/ID=([^;]*)/);}elsif ( $a[2] =~/^CDS$/i or $a[2] =~/utr/i ) {($id1) =  ($a[8] =~ m/Parent=([^;]*)/);}else{next;}if ( exists $gffs{$id1} ) {print OUT "$_\n";}}close OUT;clos...

问题 本地blast出现问题

BLAST query error: CFastaReader: Near line 2, there's a line that doesn't look like plausible data, but it's not marked as defline or comment.

文章 BSA分析中MutMap 分析：95% 99%阈值置信区间是如何计算的

...RIL"){x<-runif(1) if (x<=0.5){count<-1}else{count<-0} }else{for(i in 1:2){x<-runif(1) if (x<=0.5){number<-0.5}else{number<-0} if(number == 0.5){count<- count+0.5}}}return(count)}#######################################################################caluclate of genotyp...

文章 文本去重并统计重复次数

...one of Apple company. Hello World. The Iphone of Apple company. My name is Friendfish. Hello World. Apple and Nokia. 命令如下：$ sort test.txt | uniq -c | sort -rn 4 Hello World. 2 The Iphone of Apple company. 2 Apple and Nokia. 1 My name is Friendfish.uniq命令加-c选项可以实...

文章 perl语言标量SCALAR

...量赋值与内插，变量赋值用=； $var ="str";   #赋值print "this is $var"  #内插 ; -> '' this is str" perl遵循最长匹配，当$var 和 $varing 都存在时，print "varing" ，匹配$varing  不匹配$var 想匹配$var需要这样：${var}ing          sh中$(ls)  ...

文章 R语言跑循环，如何跳过报错信息？

...，接着执行下一次循环指令呢，可以使用try（）函数： for () {   err = try(想要执行的函数体)}#比如：for (i in 1:length(flies)) {   err = try(eQTpLot(GWAS.df = GWASdata, eQTL.df = eQTLdata , Genes.df = genedata, gene =max_r_gene,           gbuild = "hg19",  t...

文章 蛋白质比对结果快速分类taxid

...output_filename, "wb"); if (!fp) { perror("Failed to open file for writing"); return NULL; } struct my_struct *current_item, *tmp; int count = 0; HASH_ITER(hh, hash_table, current_item, tmp) { fwrite(current_item->accession, sizeof(current_item->acc...

文章 将fasta序列多行变单行——使用 awk 或 seqkit 或 python

...比较快） awk '{if($0~/>/) name=$0 ;else seq[name]=seq[name]$0;}END{for(i in seq) print i"\n"seq[i]}}' test.fa>seq1ATTAAAGGTTTATACCTTCCAATCTGTGTGGCTGTCACTCACACGAGTAACTCGTCTATC>seq2ATTAAAGGTTTATACCTTCCAATCTGTGTGGCTGTCACTC 方法二：seqkit工具 将多行序列转换为一行序列 ...

文章 scanpy 中 ScTransform分析：

...： import scanpy as scfrom scipy.sparse import issparsedef pyScTransform(adata, output_file=None):    """    Function to call scTransform from Python    """    import rpy2.robjects as ro    import anndata2ri    ro.r('library(Seurat)')    ro.r('library(scater)')    anndata2ri.act...