Question

假设我有一个DNA序列。我想得到它的补充。我使用了以下代码，但我没有得到它。我做错了什么？

s=readline()
ATCTCGGCGCGCATCGCGTACGCTACTAGC
p=unlist(strsplit(s,""))
h=rep("N",nchar(s))
unlist(lapply(p,function(d){
for b in (1:nchar(s)) {    
    if (p[b]=="A") h[b]="T"
    if (p[b]=="T") h[b]="A"
    if (p[b]=="G") h[b]="C"
    if (p[b]=="C") h[b]="G"
}

Answer 1

使用为此目的而构建的chartr：

> s
[1] "ATCTCGGCGCGCATCGCGTACGCTACTAGC"
> chartr("ATGC","TACG",s)
[1] "TAGAGCCGCGCGTAGCGCATGCGATGATCG"

给它两个等长的字符串和你的字符串。同时对翻译论证进行了矢量化：

> chartr("ATGC","TACG",c("AAAACG","TTTTT"))
[1] "TTTTGC" "AAAAA"

注意我正在替换DNA的字符串表示而不是矢量。为了转换向量，我创建了一个查找映射作为命名向量和索引：

> p
 [1] "A" "T" "C" "T" "C" "G" "G" "C" "G" "C" "G" "C" "A" "T" "C" "G" "C" "G" "T"
[20] "A" "C" "G" "C" "T" "A" "C" "T" "A" "G" "C"
> map=c("A"="T", "T"="A","G"="C","C"="G")
> unname(map[p])
 [1] "T" "A" "G" "A" "G" "C" "C" "G" "C" "G" "C" "G" "T" "A" "G" "C" "G" "C" "A"
[20] "T" "G" "C" "G" "A" "T" "G" "A" "T" "C" "G"

Answer 2

Bioconductor包Biostrings为此类操作提供了许多有用的功能。安装一次：

source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings")

然后使用

library(Biostrings)
dna = DNAStringSet(c("ATCTCGGCGCGCATCGCGTACGCTACTAGC", "ACCGCTA"))
complement(dna)

Answer 3

sapply(p, switch,  "A"="T", "T"="A","G"="C","C"="G")
  A   T   C   T   C   G   G   C   G   C   G   C   A   T   C   G   C   G   T 
"T" "A" "G" "A" "G" "C" "C" "G" "C" "G" "C" "G" "T" "A" "G" "C" "G" "C" "A" 
  A   C   G   C   T   A   C   T   A   G   C 
"T" "G" "C" "G" "A" "T" "G" "A" "T" "C" "G"

如果您不想要补充名称，可以随时使用unname删除它们。

unname(sapply(p, switch,  "A"="T", "T"="A","G"="C","C"="G") )
 [1] "T" "A" "G" "A" "G" "C" "C" "G" "C" "G" "C" "G" "T" "A" "G" "C" "G" "C"
[19] "A" "T" "G" "C" "G" "A" "T" "G" "A" "T" "C" "G"
>

Answer 4

还有一个包seqinr

library(seqinr)
comp(seq) # gives complement
rev(comp(seq)) # gives the reverse complement

Biostrings具有更小的内存配置文件，但seqinr也很好，因为您可以选择基础的情况（包括混合）并将它们更改为您想要的任何内容，例如，如果您想要混合使用T和U相同的序列。 Biostrings强迫你有T或U.

Answer 5

为了补充，无论是大写还是小写，您都可以使用import json # Create some random data structure animals = zip(['dogs', 'cats', 'mice'], [124156, 858532, 812885]) data = {k:{v: {k: [v, v, v, k, v, {k: [k, k, k, k]}]}} for k, v in animals} # Create a new file, dump the data to it with open('filename.ext', 'w+') as file: json.dump(data, file, indent=4, sort_keys=False) # Open the same file, load it back as a new variable with open('filename.ext') as file: new_dictionary = json.load(file) # Make some changes to the dict new_dictionary['new_key'] = 'hello python' # Open the file back up again and rewrite the new data with open('filename.ext', 'w+') as file: json.dump(new_dictionary, file, indent=4)：

chartr()

为了更进一步并反向补充核苷酸序列，您可以使用以下功能：

n <- "ACCTGccatGCATC"
chartr("acgtACGT", "tgcaTGCA", n)
# [1] "TGGACggtaCGTAG"

Answer 6

使用r为底的答案。用一种可怕的格式写的东西，使事情变得清晰并保持一线不变。它支持大写和小写。

revc = function(s){
       paste0(
           rev(
            unlist(
             strsplit(
                chartr("ATGCatgc","TACGtacg",s)
                      , "")                        # from strsplit
                   )                               # from unlist
               )                                   # from rev
             , collapse='')                        # from paste0
       }

Answer 7

我已经使用rev(comp(seq))软件包概括了解决方案seqinr：

install.packages("devtools")
devtools::install_github("TomKellyGenetics/tktools")
tktools::revcomp(seq)

此版本与字符串输入兼容，并且已向量化以处理多个字符串的列表或向量输入。输出类应与输入匹配，包括大小写和类型。这也支持RNA和RNA输出序列中包含“ U”的输入。

> seq <- "ATCTCGGCGCGCATCGCGTACGCTACTAGC"
> revcomp(seq)
[1] "GCTAGTAGCGTACGCGATGCGCGCCGAGAT"

> seq <- c("TATAAT", "TTTCGC", "atgcat")
> revcomp(seq)
  TATAAT   TTTCGC   atgcat 
 "ATTATA" "GCGAAA" "atgcat"

请参见manual或TomKellyGenetics/tktools github软件包存储库。

补充DNA序列

7 个答案: