Question

我有三个文件：文件1 包含许多叮当声：

AGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGAUUGGUUUCCGCUUUGUUCACAGUGGCUAAGUUCUGCACCU

文件2 包含文件1中与左一侧匹配的字符串的子字符串：

AGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGAUUGGUUUCCGCUUUGUUCACAGUGGCUAAGUUCUGCACCU
      AGAGCUUAGCUGAUUGGUGAAC

文件3 包含文件1中与右侧一侧匹配的字符串的子字符串：

AGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGAUUGGUUUCCGCUUUGUUCACAGUGGCUAAGUUCUGCACCU
                                                UUCACAGUGGCUAAGUUCUGC

我想提取位于匹配

的两个字符串之间的字符串

AGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGAUUGGUUUCCGCUUUGUUCACAGUGGCUAAGUUCUGCACCU
      AGAGCUUAGCUGAUUGGUGAAC                    UUCACAGUGGCUAAGUUCUGC

输出：

                            AGUGAUUGGUUUCCGCUUUG

我想为 file 1 （约200个字符串）中的所有字符串执行此操作

示例文件1 ：

>mmu-let-7g
CCAGGCTGAGGTAGTAGTTTGTACAGTTTGAGGGTCTATGATACCACCCGGTACAGGAGATAACTGTACAGGCCACTGCCTTGCCAGG
>mmu-let-7i
CTGGCTGAGGTAGTAGTTTGTGCTGTTGGTCGGGTTGTGACATTGCCCGCTGTGGAGATAACTGCGCAAGCTACTGCCTTGCTAG
>mmu-miR-1a-1
GCTTGGGACACATACTTCTTTATATGCCCATATGAACCTGCTAAGCTATGGAATGTAAAGAAGTATGTATTTCAGGC

示例文件2 和文件3 ：

>mmu-let-7g-5p MIMAT0000121 Mus musculus let-7g-5p
UGAGGUAGUAGUUUGUACAGUU
>mmu-let-7g-3p MIMAT0004519 Mus musculus let-7g-3p
ACUGUACAGGCCACUGCCUUGC
>mmu-let-7i-5p MIMAT0000122 Mus musculus let-7i-5p
UGAGGUAGUAGUUUGUGCUGUU

Answer 1

假设你正在使用这样的东西：

file1 <- "AGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGAUUGGUUUCCGCUUUGUUCACAGUGGCUAAGUUCUGCACCU"
file2 <- "AGAGCUUAGCUGAUUGGUGAAC"
file3 <- "UUCACAGUGGCUAAGUUCUGC"

您可以尝试使用＆＃34; file2＆＃34;构建搜索模式。和＆＃34; file3＆＃34;并使用gsub。

示例：

gsub(paste0("(^.*", file2, ")(.*)(", file3, ".*)$"), "\\2", file1)
# [1] "AGUGAUUGGUUUCCGCUUUG"

Answer 2

您也可以尝试：

str1 <- "AGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGAUUGGUUUCCGCUUUGUUCACAGUGGCUAAGUUCUGCACCU"
leftstr <- "AGAGCUUAGCUGAUUGGUGAAC"
rightstr <- "UUCACAGUGGCUAAGUUCUGC"

library(qdap)
 unname(genXtract(str1,leftstr, rightstr))
#[1] "AGUGAUUGGUUUCCGCUUUG"

更新

如果您有多个字符串

 str2 <- c(str1, "AGGUGUCCCCCCUUUUUGGAGUGGCCGCUUUUGCGGGGUAAUUG")
 leftstr1 <- c(leftstr, "CCCCCUUUU")
 rightstr1 <- c(rightstr, "UUUUGCGG")
 unlist(genXtract(str2, leftstr1, rightstr1))
 #[1] "AGUGAUUGGUUUCCGCUUUG" "UGGAGUGGCCGC"

将结果与@Venkataramanan的帖子进行比较

 temp1 <- mapply(gsub, leftstr1, "|", str2)
 temp2 <- mapply(gsub, rightstr1, "|", temp1)
  unlist(strsplit(temp2, "|", fixed=T),use.names=F)[c(F,T,F)]
 #[1] "AGUGAUUGGUUUCCGCUUUG" "UGGAGUGGCCGC"

或

   scan(text=gsub(paste(rightstr1, collapse="|"),
  " ",gsub(paste(leftstr1,collapse="|")," ",str2)),
  what="character")[c(F,T,F)]
#Read 6 items
# [1] "AGUGAUUGGUUUCCGCUUUG" "UGGAGUGGCCGC"

或

 library(stringr)
  str_extract_all(str1, perl(paste0("(?<=",leftstr,")",".*(?=", rightstr,")")))[[1]]
 #[1] "AGUGAUUGGUUUCCGCUUUG"

Answer 3

以下代码完成了这项工作：

temp1<- gsub("AGAGCUUAGCUGAUUGGUGAAC", "|", "AGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGAUUGGUUUCCGCUUUGUUCACAGUGGCUAAGUUCUGCACCU")
temp1
temp2<- gsub("UUCACAGUGGCUAAGUUCUGC","|", temp1)
temp2
unlist(strsplit(temp2, "|", fixed=T))[2]

选择两个匹配字符串之间的子串

3 个答案:

更新