Question

我有一些要在R中重新格式化的序列。

但是R向我展示了行返回的序列（如<router-link :to="{ name: 'listings' }" exact>Listings</router-link>所示：

"\n"

但是我要删除所有seqs <- ">PRTRE213-13 Volkameria aculeatum matK \n------------------------------------------------------------------CCAAC\nCGAGAGCCAGCTCC------TCTTTTTCAAAA---------CGAAAT---------------------CAA\nAAGACTATTCTTATTCTTATAT------------AATTCTCATGTATGTGAATATGAATCCGTTTTCGTCT\nTTTCTACGTAACCAATCTTTT---CATTTACGATCAACATCTTTTGAAGTTCTTCTTGAACGAATCTATTT\nTCTATGTA---------AAAGTAGAACGTCTT------GTGAACGTCTTTGTTAAGATTAAC---------\n-AATTTTCGGGCGAACCCGTGGTTGGTCAAG------GAACCTTTCATGCATTATATTAGGTATCAAAGAA\nAGATCCATTCTGGCTTCA------AAGGGAACATCTTTTTTCATGAAAAAATGGCAATTTTATCTTGTCAC\nCTTTTTGGCAATGGCATTTTTCGCTGTGGTTTCATCCAAGAAGGATTTATCTAAAC---CAATTATCCAAT\nTTATTCCCTTGAA------TTTTTGGGCTATCTTTCA------AGCGTGCGAATGAACCCCTCTGTGGTAC\nCGGAGTCAAATTCTAGAAAATGCATTTCTAATCAATAATGCTATT------AAGAAGTTTGATACCCTTAT\nTTCCAATTATTCCAATGATTGCGTCATTGGCTAAAGCGAAATTTTGTAACGTATTTGGGCATCCTGTTAGT\nTAAGCCGATTTGGGCTGATTTATCAGATTCTAATATTATTGACCGATTTGGTCGTATA---TGCAGAAATC\nCTTTCTC-------------" 的第一个。即：

\n

如果我这样做，它将删除所有退货。

[1] ">PRTRE213-13 Volkameria aculeatum matK \n------------------------------------------------------------------CCAACCGAGAGCCAGCTCC------TCTTTTTCAAAA---------CGAAAT---------------------CAAAAGACTATTCTTATTCTTATAT------------AATTCTCATGTATGTGAATATGAATCCGTTTTCGTCTTTTCTACGTAACCAATCTTTT---CATTTACGATCAACATCTTTTGAAGTTCTTCTTGAACGAATCTATTTTCTATGTA---------AAAGTAGAACGTCTT------GTGAACGTCTTTGTTAAGATTAAC----------AATTTTCGGGCGAACCCGTGGTTGGTCAAG------GAACCTTTCATGCATTATATTAGGTATCAAAGAAAGATCCATTCTGGCTTCA------AAGGGAACATCTTTTTTCATGAAAAAATGGCAATTTTATCTTGTCACCTTTTTGGCAATGGCATTTTTCGCTGTGGTTTCATCCAAGAAGGATTTATCTAAAC---CAATTATCCAATTTATTCCCTTGAA------TTTTTGGGCTATCTTTCA------AGCGTGCGAATGAACCCCTCTGTGGTACCGGAGTCAAATTCTAGAAAATGCATTTCTAATCAATAATGCTATT------AAGAAGTTTGATACCCTTATTTCCAATTATTCCAATGATTGCGTCATTGGCTAAAGCGAAATTTTGTAACGTATTTGGGCATCCTGTTAGTTAAGCCGATTTGGGCTGATTTATCAGATTCTAATATTATTGACCGATTTGGTCGTATA---TGCAGAAATCCTTTCTC-------------"

这不起作用：

gsub(pattern = "\n",replacement = "", x = seqs)

这给了我一个错误：

sub("^(.*? \n .*?) \n .*", "\\1", seqs)

我的序列是可变的：

gsub(pattern = "${'\n'[*]:0:2}",replacement = "", x = seqs)
Error in gsub(pattern = "${'\n'[*]:0:2}", replacement = "", x = seqs) : 
  invalid regular expression '${'
'[*]:0:2}', reason 'Invalid contents of {}'

最终结果将是

">Whatever here before \n the sequence start \n the rest \n..."

有趣的是，下面的代码部分适用于测试语句，但不适用于上面的序列：

">Whatever here before \n the sequence start the rest..."

Answer 1

像这样尝试：

seqs <- ">PRTRE213-13 Volkameria aculeatum matK \n------------------------------------------------------------------CCAAC\nCGAGAGCCAGCTCC------TCTTTTTCAAAA---------CGAAAT---------------------CAA\nAAGACTATTCTTATTCTTATAT------------AATTCTCATGTATGTGAATATGAATCCGTTTTCGTCT\nTTTCTACGTAACCAATCTTTT---CATTTACGATCAACATCTTTTGAAGTTCTTCTTGAACGAATCTATTT\nTCTATGTA---------AAAGTAGAACGTCTT------GTGAACGTCTTTGTTAAGATTAAC---------\n-AATTTTCGGGCGAACCCGTGGTTGGTCAAG------GAACCTTTCATGCATTATATTAGGTATCAAAGAA\nAGATCCATTCTGGCTTCA------AAGGGAACATCTTTTTTCATGAAAAAATGGCAATTTTATCTTGTCAC\nCTTTTTGGCAATGGCATTTTTCGCTGTGGTTTCATCCAAGAAGGATTTATCTAAAC---CAATTATCCAAT\nTTATTCCCTTGAA------TTTTTGGGCTATCTTTCA------AGCGTGCGAATGAACCCCTCTGTGGTAC\nCGGAGTCAAATTCTAGAAAATGCATTTCTAATCAATAATGCTATT------AAGAAGTTTGATACCCTTAT\nTTCCAATTATTCCAATGATTGCGTCATTGGCTAAAGCGAAATTTTGTAACGTATTTGGGCATCCTGTTAGT\nTAAGCCGATTTGGGCTGATTTATCAGATTCTAATATTATTGACCGATTTGGTCGTATA---TGCAGAAATC\nCTTTCTC-------------"
gsub(pattern = "(^.*?\\n)|\\n",replacement = "\\1", x = seqs, perl = TRUE)

regex101 demo

正则表达式的想法

(^.*?\\n)|\\n

捕获到组中第一个换行符之前的所有内容，以保留并放回替换行中。

Answer 2

一种stringr方法，可以简单地分割字符串并将两部分重新组合在一起。

seqs <- ">PRTRE213-13 Volkameria aculeatum matK \n------------------------------------------------------------------CCAAC\nCGAGAGCCAGCTCC------TCTTTTTCAAAA---------CGAAAT---------------------CAA\nAAGACTATTCTTATTCTTATAT------------AATTCTCATGTATGTGAATATGAATCCGTTTTCGTCT\nTTTCTACGTAACCAATCTTTT---CATTTACGATCAACATCTTTTGAAGTTCTTCTTGAACGAATCTATTT\nTCTATGTA---------AAAGTAGAACGTCTT------GTGAACGTCTTTGTTAAGATTAAC---------\n-AATTTTCGGGCGAACCCGTGGTTGGTCAAG------GAACCTTTCATGCATTATATTAGGTATCAAAGAA\nAGATCCATTCTGGCTTCA------AAGGGAACATCTTTTTTCATGAAAAAATGGCAATTTTATCTTGTCAC\nCTTTTTGGCAATGGCATTTTTCGCTGTGGTTTCATCCAAGAAGGATTTATCTAAAC---CAATTATCCAAT\nTTATTCCCTTGAA------TTTTTGGGCTATCTTTCA------AGCGTGCGAATGAACCCCTCTGTGGTAC\nCGGAGTCAAATTCTAGAAAATGCATTTCTAATCAATAATGCTATT------AAGAAGTTTGATACCCTTAT\nTTCCAATTATTCCAATGATTGCGTCATTGGCTAAAGCGAAATTTTGTAACGTATTTGGGCATCCTGTTAGT\nTAAGCCGATTTGGGCTGATTTATCAGATTCTAATATTATTGACCGATTTGGTCGTATA---TGCAGAAATC\nCTTTCTC-------------"

library(stringr)

keep_first_newline <- function(string){
  first_newline <- str_locate(string, "\\n")[1]
  head <-  str_sub(string, end = first_newline)
  tail = string %>%
    str_sub(start = first_newline + 1) %>%
    str_remove_all("\\n")
  out <- str_c(head, tail)
}

seqs %>%
  keep_first_newline %>%
  writeLines
#> >PRTRE213-13 Volkameria aculeatum matK 
#> ------------------------------------------------------------------CCAACCGAGAGCCAGCTCC------TCTTTTTCAAAA---------CGAAAT---------------------CAAAAGACTATTCTTATTCTTATAT------------AATTCTCATGTATGTGAATATGAATCCGTTTTCGTCTTTTCTACGTAACCAATCTTTT---CATTTACGATCAACATCTTTTGAAGTTCTTCTTGAACGAATCTATTTTCTATGTA---------AAAGTAGAACGTCTT------GTGAACGTCTTTGTTAAGATTAAC----------AATTTTCGGGCGAACCCGTGGTTGGTCAAG------GAACCTTTCATGCATTATATTAGGTATCAAAGAAAGATCCATTCTGGCTTCA------AAGGGAACATCTTTTTTCATGAAAAAATGGCAATTTTATCTTGTCACCTTTTTGGCAATGGCATTTTTCGCTGTGGTTTCATCCAAGAAGGATTTATCTAAAC---CAATTATCCAATTTATTCCCTTGAA------TTTTTGGGCTATCTTTCA------AGCGTGCGAATGAACCCCTCTGTGGTACCGGAGTCAAATTCTAGAAAATGCATTTCTAATCAATAATGCTATT------AAGAAGTTTGATACCCTTATTTCCAATTATTCCAATGATTGCGTCATTGGCTAAAGCGAAATTTTGTAACGTATTTGGGCATCCTGTTAGTTAAGCCGATTTGGGCTGATTTATCAGATTCTAATATTATTGACCGATTTGGTCGTATA---TGCAGAAATCCTTTCTC-------------

由reprex package（v0.2.0）于2018-06-29创建。

Answer 3

使用gsubfn，我们可以做到。在这种情况下，没有什么比正则表达式更好，但是如果您想将第一个n出现在n>1中，则更容易扩展。

library(gsubfn)
p <- proto(fun = function(this, x) if(count > 1) '' else x)
out <- gsubfn('\n', p, seqs)

与接受的答案相同

out == gsub(pattern = "(^.*?\\n)|\\n",replacement = "\\1", x = seqs, perl = TRUE)
#[1] TRUE

从第二个“ \ n”和其余的字符串中删除返回的字符串（不要删除第一个）

3 个答案: