如何使用 R 在另一个特定模式之前提取两个特定模式？答案

【问题标题】：How to extract two specific patterns before another specific pattern using R?如何使用 R 在另一个特定模式之前提取两个特定模式？
【发布时间】：2021-11-04 13:31:20
【问题描述】：

我正在尝试提取一个字母（应该是 K 或 Y）以及该字母与模式 (XO44_TMT6) 之间的所有数字，并将提取的值放在两个单独的列中（Mod.residue 和 Mod.position.in.pep），但失败了得到我想要的。

以下是我的代码和数据框。谁能解释我的代码失败的原因以及如何解决？

非常感谢！

我的数据框：

structure(list(Modifications = c("Y9(XO44_TMT6)", "Y9(XO44_TMT6)", 
"Y9(XO44_TMT6)", "Y9(XO44_TMT6)", "Y9(XO44_TMT6)", "Y9(XO44_TMT6)", 
"Y9(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", 
"Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", 
"Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", 
"Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", "Y8(XO44_TMT6)", 
"Y8(XO44_TMT6)", "Y7(XO44_TMT6); M9(Oxidation)", "Y7(XO44_TMT6); M8(Oxidation)", 
"Y7(XO44_TMT6); M8(Oxidation)", "Y7(XO44_TMT6); C9(Carbamidomethyl); C18(Carbamidomethyl)", 
"Y7(XO44_TMT6); C15(Carbamidomethyl)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", "Y7(XO44_TMT6)", 
"Y6(XO44_TMT6); C23(Carbamidomethyl)", "Y6(XO44_TMT6); C12(Carbamidomethyl)", 
"Y6(XO44_TMT6); C12(Carbamidomethyl)", "Y6(XO44_TMT6)", "Y6(XO44_TMT6)", 
"Y6(XO44_TMT6)", "Y6(XO44_TMT6)", "Y6(XO44_TMT6)", "Y6(XO44_TMT6)", 
"Y6(XO44_TMT6)", "Y6(XO44_TMT6)", "Y6(XO44_TMT6)", "Y6(XO44_TMT6)", 
"Y6(XO44_TMT6)", "Y6(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", 
"Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", 
"Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", 
"Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", 
"Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y5(XO44_TMT6)", "Y4(XO44_TMT6); C29(Carbamidomethyl)", 
"Y4(XO44_TMT6); C13(Carbamidomethyl)", "Y4(XO44_TMT6)", "Y4(XO44_TMT6)", 
"Y4(XO44_TMT6)", "Y4(XO44_TMT6)", "Y4(XO44_TMT6)", "Y4(XO44_TMT6)", 
"Y4(XO44_TMT6)", "Y4(XO44_TMT6)", "Y4(XO44_TMT6)", "Y4(XO44_TMT6)", 
"Y4(XO44_TMT6)", "Y3(XO44_TMT6); M5(Oxidation)", "Y3(XO44_TMT6); C11(Carbamidomethyl)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", "Y3(XO44_TMT6)", 
"Y29(XO44_TMT6)", "Y25(XO44_TMT6)", "Y25(XO44_TMT6)", "Y25(XO44_TMT6)", 
"Y23(XO44_TMT6)", "Y22(XO44_TMT6)", "Y22(XO44_TMT6)", "Y22(XO44_TMT6)", 
"Y22(XO44_TMT6)", "Y22(XO44_TMT6)", "Y22(XO44_TMT6)", "Y22(XO44_TMT6)", 
"Y21(XO44_TMT6)", "Y20(XO44_TMT6)", "Y20(XO44_TMT6)", "Y20(XO44_TMT6)", 
"Y20(XO44_TMT6)", "Y20(XO44_TMT6)", "Y20(XO44_TMT6)", "Y20(XO44_TMT6)", 
"Y20(XO44_TMT6)", "Y2(XO44_TMT6); C8(Carbamidomethyl)", "Y2(XO44_TMT6); C19(Carbamidomethyl)", 
"Y2(XO44_TMT6); C15(Carbamidomethyl)", "Y2(XO44_TMT6); C15(Carbamidomethyl)", 
"Y2(XO44_TMT6); C15(Carbamidomethyl)", "Y2(XO44_TMT6); C15(Carbamidomethyl)", 
"Y2(XO44_TMT6); C15(Carbamidomethyl)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", 
"Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", 
"Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", 
"Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y2(XO44_TMT6)", 
"Y2(XO44_TMT6)", "Y2(XO44_TMT6)", "Y19(XO44_TMT6)", "Y19(XO44_TMT6)", 
"Y19(XO44_TMT6)", "Y19(XO44_TMT6)", "Y19(XO44_TMT6)", "Y18(XO44_TMT6)", 
"Y18(XO44_TMT6)", "Y18(XO44_TMT6)", "Y18(XO44_TMT6)", "Y18(XO44_TMT6)", 
"Y18(XO44_TMT6)", "Y18(XO44_TMT6)", "Y17(XO44_TMT6)", "Y17(XO44_TMT6)", 
"Y17(XO44_TMT6)", "Y17(XO44_TMT6)", "Y17(XO44_TMT6)", "Y16(XO44_TMT6)", 
"Y16(XO44_TMT6)", "Y16(XO44_TMT6)", "Y16(XO44_TMT6)", "Y16(XO44_TMT6)", 
"Y16(XO44_TMT6)", "Y16(XO44_TMT6)", "Y16(XO44_TMT6)", "Y16(XO44_TMT6)", 
"Y16(XO44_TMT6)", "Y15(XO44_TMT6); C16(Carbamidomethyl)", "Y15(XO44_TMT6)", 
"Y15(XO44_TMT6)", "Y15(XO44_TMT6)", "Y15(XO44_TMT6)", "Y15(XO44_TMT6)", 
"Y15(XO44_TMT6)", "Y15(XO44_TMT6)", "Y15(XO44_TMT6)", "Y15(XO44_TMT6)", 
"Y14(XO44_TMT6); C15(Carbamidomethyl)", "Y14(XO44_TMT6); C15(Carbamidomethyl)", 
"Y14(XO44_TMT6)", "Y14(XO44_TMT6)", "Y14(XO44_TMT6)", "Y13(XO44_TMT6)", 
"Y13(XO44_TMT6)", "Y13(XO44_TMT6)", "Y12(XO44_TMT6); C14(Carbamidomethyl)", 
"Y12(XO44_TMT6)", "Y12(XO44_TMT6)", "Y12(XO44_TMT6)", "Y12(XO44_TMT6)", 
"Y12(XO44_TMT6)", "Y12(XO44_TMT6)", "Y12(XO44_TMT6)", "Y12(XO44_TMT6)", 
"Y12(XO44_TMT6)", "Y12(XO44_TMT6)", "Y12(XO44_TMT6)", "Y12(XO44_TMT6)", 
"Y11(XO44_TMT6)", "Y11(XO44_TMT6)", "Y11(XO44_TMT6)", "Y11(XO44_TMT6)", 
"Y11(XO44_TMT6)", "Y11(XO44_TMT6)", "Y11(XO44_TMT6)", "Y10(XO44_TMT6)", 
"Y10(XO44_TMT6)", "Y10(XO44_TMT6)", "Y10(XO44_TMT6)", "Y10(XO44_TMT6)", 
"Y10(XO44_TMT6)", "Y10(XO44_TMT6)", "Y10(XO44_TMT6)", "Y10(XO44_TMT6)", 
"Y10(XO44_TMT6)", "Y10(XO44_TMT6)", "Y10(XO44_TMT6)", "Y1(XO44_TMT6); C9(Carbamidomethyl)", 
"Y1(XO44_TMT6); C15(Carbamidomethyl)", "Y1(XO44_TMT6); C15(Carbamidomethyl)", 
"Y1(XO44_TMT6); C15(Carbamidomethyl)", "Y1(XO44_TMT6); C15(Carbamidomethyl)", 
"Y1(XO44_TMT6); C11(Carbamidomethyl)", "Y1(XO44_TMT6); C11(Carbamidomethyl)", 
"Y1(XO44_TMT6); C11(Carbamidomethyl)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", 
"Y1(XO44_TMT6)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", 
"Y1(XO44_TMT6)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", 
"Y1(XO44_TMT6)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", "Y1(XO44_TMT6)", 
"Y1(XO44_TMT6)", "N-Term(Prot)(Met-loss+Acetyl); Y9(XO44_TMT6)", 
"N-Term(Prot)(Met-loss+Acetyl); Y9(XO44_TMT6)", "N-Term(Prot)(Met-loss+Acetyl); Y9(XO44_TMT6)", 
"N-Term(Prot)(Met-loss+Acetyl); Y9(XO44_TMT6)", "N-Term(Prot)(Met-loss+Acetyl); Y8(XO44_TMT6)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6); C17(Carbamidomethyl)", 
"N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6)", "N-Term(Prot)(Met-loss+Acetyl); Y7(XO44_TMT6)", 
"N-Term(Prot)(Met-loss+Acetyl); K4(XO44_TMT6)", "N-Term(Prot)(Met-loss); Y8(XO44_TMT6)", 
"N-Term(Prot)(Met-loss); Y8(XO44_TMT6)", "N-Term(Prot)(Met-loss); Y8(XO44_TMT6)", 
"N-Term(Prot)(Met-loss); Y8(XO44_TMT6)"), Mod.residue = c("9", 
"9", "9", "9", "9", "9", "9", "8", "8", "8", "8", "8", "8", "8", 
"8", "8", "8", "8", "8", "8", "8", "8", "8", "7", "7", "7", "7", 
"7", "7", "7", "7", "7", "7", "7", "7", "7", "7", "7", "7", "7", 
"7", "7", "7", "7", "7", "7", "7", "7", "7", "7", "7", "7", "7", 
"7", "6", "6", "6", "6", "6", "6", "6", "6", "6", "6", "6", "6", 
"6", "6", "6", "5", "5", "5", "5", "5", "5", "5", "5", "5", "5", 
"5", "5", "5", "5", "5", "5", "5", "4", "4", "4", "4", "4", "4", 
"4", "4", "4", "4", "4", "4", "4", "3", "3", "3", "3", "3", "3", 
"3", "3", "3", "3", "3", "3", "3", "3", "3", "3", "3", "3", "3", 
"3", "3", "3", "3", "3", "3", "3", "3", "3", "3", "3", "9", "5", 
"5", "5", "3", "2", "2", "2", "2", "2", "2", "2", "1", "0", "0", 
"0", "0", "0", "0", "0", "0", "2", "2", "2", "2", "2", "2", "2", 
"2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", "2", 
"2", "2", "2", "9", "9", "9", "9", "9", "8", "8", "8", "8", "8", 
"8", "8", "7", "7", "7", "7", "7", "6", "6", "6", "6", "6", "6", 
"6", "6", "6", "6", "5", "5", "5", "5", "5", "5", "5", "5", "5", 
"5", "4", "4", "4", "4", "4", "3", "3", "3", "2", "2", "2", "2", 
"2", "2", "2", "2", "2", "2", "2", "2", "2", "1", "1", "1", "1", 
"1", "1", "1", "0", "0", "0", "0", "0", "0", "0", "0", "0", "0", 
"0", "0", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1", 
"1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "1", "9", 
"9", "9", "9", "8", "7", "7", "7", "7", "7", "7", "7", "7", "7", 
"7", "7", "7", "7", "7", "7", "7", "7", "4", "8", "8", "8", "8"
), Mod.position.in.pep = c("", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "", "", "", "", "", "", "", "", "", "", "", "", "", "", 
"", "", "")), row.names = c(NA, -300L), class = "data.frame")

我的代码：

df <- df.test %>% 
  mutate(Mod.residue = gsub(".*(\\w{1})\\d*\\(XO44_TMT6)\\;*\\s*.*", "\\1", Modifications),
         Mod.position.in.pep = gsub(".*\\w{1}(\\d*)\\(XO44_TMT6\\)\\;*\\s*.*", "\\1", Modifications)
           )

【问题讨论】：

我刚刚意识到我已经回答了您的一个（不同）问题，即跨栏文本的分离/连接。我强烈建议您掌握 AWESOME tidyr 包：tidyr.tidyverse.org 对于字符串操作，我还认为 stringr 比基本 R 函数更一致且更易于使用：stringr.tidyverse.org
非常感谢您的推荐！将学习如何使用tidyr 包。
我刚刚发布了一个后续的类似问题，以查看 somone 是否提出了更好的建议：stackoverflow.com/questions/69095697/…

标签： r regex tidyr

【解决方案1】：

我认为您正在寻找 tidyr::extract，它在单个函数调用中非常适合您的目的。

library(tidyr)

output_extract<-df %>%
        extract(Modifications,
               into = c('Mod.residue', 'Mod.position.in.pep'),
               regex = ".*([A-Z])(\\d+)(?=\\(XO44_TMT6\\)).*",
               remove=FALSE)

如果你想继续使用gsub，你可以这样做（相同的模式，两个不同的替换（\\1和\\2）：

output_gsub<-df %>% mutate(Mod.residue=gsub(".*([A-Z])(\\d+)(\\(XO44_TMT6\\)).*", "\\1", Modifications),
              Mod.position.in.pep=gsub(".*([A-Z])(\\d+)(\\(XO44_TMT6\\)).*", "\\2", Modifications))

这些方法给出相同的输出：

identical(output_extract, output_gsub)

[1] TRUE

您可能希望之后使用as.numeric 将“Mod.position.in.pep”变量转换为数字。

输出列的唯一值：

$Mod.residue
[1] "Y" "K"

$Mod.position.in.pep
 [1] "9"  "8"  "7"  "6"  "5"  "4"  "3"  "29" "25" "23" "22" "21" "20" "2"  "19" "18" "17" "16" "15" "14" "13" "12" "11" "10" "1"

编辑

这仅适用于“Mod.residue”或“Mod.position.in.pep”的单一匹配项。

如果每次观察有多个“[KY]digit(XO44_TMT6)”，则可能需要采用更复杂的方法，即mutate %>% unnest_wider %>% unite

#Example data
df<-tibble(Modifications="K4(XO44_TMT6); Y6(XO44_TMT6)")

#solution
library(dplyr)
library(tidyr)
library(stringr)

df %>% mutate(Mod.residue=str_extract_all(Modifications, "[A-Z]+(?=\\d+\\(XO44_TMT6\\))"),
              Mod.position.in.pep=str_extract_all(Modifications, "\\d+(?=\\(XO44_TMT6\\))"))%>%
        unnest_wider(col='Mod.residue', names_sep = "_")%>%
        unnest_wider(col='Mod.position.in.pep', names_sep = "_")%>%
        unite(starts_with('Mod.residue'), col="Mod.residue", sep = ';', remove=TRUE, na.rm=TRUE)%>%
        unite(starts_with('Mod.position'), col='Mod.position.in.pep', sep=';', remove=TRUE, na.rm=TRUE)

输出

# A tibble: 1 x 3
  Modifications                Mod.residue Mod.position.in.pep
  <chr>                        <chr>       <chr>              
1 K4(XO44_TMT6); Y6(XO44_TMT6) K;Y         4;6

【讨论】：

感谢您的回答！例如，如果Y2(XO44_TMT6) 在C19(Carbamidomethyl); 之前，您的代码就可以工作，但在C19(Carbamidomethyl); Y2(XO44_TMT6) 的情况下就不能工作。不过很容易修复。
你知道如何用gsub提取我想要的东西吗？
获得了 gsub 的正则表达式。更新。处理extract
extract 现在也很好，@Dr。化学生物
你必须添加一个na.rm=TRUE 参数到unite() 更新

【解决方案2】：

我将首先创建一个列，其中包含整个残基。位置被提取。然后你可以根据这个列将名称和位置分开，然后删除中间结果：

df.test %>% 
  mutate(
    residue = Modifications %>% str_extract("[KY][0-9]+"),
    Mod.residue = residue %>% str_extract("^[KY]"),
    Mod.position.in.pep = residue %>% str_extract("[0-9]") %>% as.numeric(),
  ) %>%
  select(-residue)

str_extract 旨在与其他 tidyverse 函数一起使用。

【讨论】：

谢谢！你知道如何用gsub提取我想要的吗？
gsub 用于替换而不是用于提取字符串。