Question

我在R（3.2.3）

中运行此代码

outfolder <- "CAI_inter_domains_ENA/"  
if (!file.exists(outfolder))dir.create(outfolder)

genome.and.organisms <- read.csv(file = "test_genomes_ENA10.csv", header = FALSE, 
                             as.is=TRUE) 


# calculating the codon adaptation index for all genomes and its domains

for (genomeID in genome.and.organisms[,1]) { 
fileout <- paste(outfolder, genomeID, "_CAI_inter.csv", sep="")
 #check if file already exists
if (!file.exists(fileout)) {
 # Going through all genome numbers and retrieving their weight vectors and domain data
  w.files <- paste("Reference_weight_tables_ENA/", genomeID, ".csv", sep = "")
if (file.exists(w.files)){
  w.data <- read.csv(file = w.files, header = FALSE, as.is = TRUE)
  # ordering on rownames, for it to be correctly used by cai function
  ordered.w <- w.data[with(w.data, order(V1)), ]
  # only leaving numbers
  w <- ordered.w[,2]
  domain.files <- paste("Domain_data_ENA/", genomeID, ".csv", sep = "")
  domain.data <- read.csv(file = domain.files, header = TRUE, 
                          as.is=TRUE)

 #alot of different stuff happens here..
 #like making dataframes
 # these are written to a file


write.table(domain.data.CDS, file = "tmp.csv", append = FALSE, sep = ",", row.names = FALSE, quote = FALSE, col.names = FALSE)

  # converting the sequences to fasta format with python file
  convertcmd <- "python Write_csvtofasta.py"
  system(convertcmd)

  # opening the written file and calculating the CAI
    fasta.domains <- read.fasta(file = "tmp.fasta")
    cai.inter.output <- sapply(fasta.domains, cai, w = w)
    write.table(cai.inter.output, file = fileout, append = F, sep = ",", 
    row.names = names(cai.inter.output), quote = F, col.names = F)
  }

代码工作正常，直到它使用“cai”函数的部分，在那里它抛出了我的错误，我不知道我该怎么做才能解决它：

Error in seq.default(from = frame + 1, to = length(seq), by = word) : 
wrong sign in 'by' argument

tmp.fasta是一个fasta文件，其中包含大量的fasta序列，就像通常的fasta文件格式一样：（http://bioinformatics.intec.ugent.be/MotifSuite/images/Fasta.png）

for循环仅适用于某些基因组ID，因为我试图将输入文件“test_genomes_ENA10.csv”更改为只有一个基因组ID。

我试图更仔细地查看seq.default函数，这一行会引发错误：

if (n < 0L) 
    stop("wrong sign in 'by' argument")

但是当我调查这个if语句如何被评估为真时，对我来说是一个谜。

这里的任何人都可以帮我解决这个神秘的错误吗？

聚苯乙烯。功能

cai

来自“seqinr”包

seq.default出错：'by'参数

0 个答案: