在两个匹配字符串之间选择子字符串 [英] select substring between two matching strings

问题描述

我有三个文件:文件 1 包含许多如下所示的字符串:

I have three files: File 1 contains a number of stings like below:

AGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGAUUGGUUUCCGCUUUGUUCACAGUGGCUAAGUUCUGCACCU

文件 2 包含文件 1 中与左侧匹配的字符串的子字符串:

File 2 contains a substring of the string in file 1 matching the left side:

AGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGAUUGGUUUCCGCUUUGUUCACAGUGGCUAAGUUCUGCACCU
      AGAGCUUAGCUGAUUGGUGAAC  

文件 3 包含文件 1 中与右侧匹配的字符串的子字符串:

File 3 contains a substring of the string in file 1 matching the right side:

AGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGAUUGGUUUCCGCUUUGUUCACAGUGGCUAAGUUCUGCACCU
                                                UUCACAGUGGCUAAGUUCUGC

我想提取位于匹配的两个字符串之间的字符串

I want to extract the string that lies between the two strings that match

AGGUGCAGAGCUUAGCUGAUUGGUGAACAGUGAUUGGUUUCCGCUUUGUUCACAGUGGCUAAGUUCUGCACCU
      AGAGCUUAGCUGAUUGGUGAAC                    UUCACAGUGGCUAAGUUCUGC

输出:

                            AGUGAUUGGUUUCCGCUUUG

我想对文件 1 中的所有字符串执行此操作(大约 200 个字符串)

I would like to do this for all my strings in file 1 (approx 200 strings)

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

推荐答案

你也可以试试:

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

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

更新

如果你有多个字符串

Update

If you have multiple strings

 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

Comparing the results with @Venkataramanan's post

 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"

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