提取特定词

Question

我有这个对象列表：

  dput(head(annotations))
    structure(list(X1 = c("KQ415659.1", "KQ415659.1", "KQ415659.1", 
    "KQ415659.1", "KQ415659.1", "KQ415659.1"), X2 = c("Genbank", 
    "Genbank", "Genbank", "Genbank", "Genbank", "Genbank"), X3 = c("exon", 
    "exon", "exon", "exon", "exon", "exon"), X4 = c(2986, 8779, 12123, 
    14982, 15303, 15780), X5 = c(3040, 8886, 12182, 15050, 15387, 
    15844), X6 = c(".", ".", ".", ".", ".", "."), X7 = c("+", "+", 
    "+", "+", "+", "+"), X8 = c(".", ".", ".", ".", ".", "."), X9 = c("transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028242mg\";", 
    "transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028243mg\";", 
    "transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028244mg\";", 
    "transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028245mg\";", 
    "transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028246mg\";", 
    "transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028247mg\";"
    )), class = c("tbl_df", "tbl", "data.frame"), row.names = c(NA, 
    -6L))

我想从所有字符串中提取以"ICBIM"开头并以"mg"结尾的单词。

# A tibble: 6 x 1
  X9                                                                          
<chr>
        1 "transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028241mg\";"
        2 "transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028242mg\";"
        3 "transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028243mg\";"
        4 "transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028244mg\";"
        5 "transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028245mg\";"
        6 "transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028246mg\";"

Answer 1

starts with "ICBIM" and ends with "mg"

ICBIM.+?mg

See the regex demo

Answer 2

您可以在 sub:

中使用此正则表达式

sub(".*\b(ICBIM.+mg)\b.*", "\1", annotations$X9)
# [1] "ICBIM_22028242mg" "ICBIM_22028243mg" "ICBIM_22028244mg" "ICBIM_22028245mg"
# [5] "ICBIM_22028246mg" "ICBIM_22028247mg"

这里，\b表示文字边框。

Answer 3

R 中的正则表达式匹配有点奇怪。你有 6 个函数（grep、grepl、sub、gsub、regexpr、gregepr、regexec）做相关的东西，但是 none 其中 returns 是实际的字符串。您可以获得的最接近的东西是来自（例如）regexpr 的匹配位置和长度列表，可以传递给 regmatches 以获取字符串。

所以我会这样做：

your_data = c("transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028241mg\";", "transcript_id \"rna0\"; gene_id \"gene0\"; gene_name \"ICBIM_22028242mg\";")
matches = regexpr("ICBIM.*mg", your_data)
regmatches(your_data, matches)
[1] "ICBIM_22028241mg" "ICBIM_22028242mg"

Answer 4

假设行的格式相同，没有 regex:

substring(annotations$X9, 51, 66)
# [1] "ICBIM_22028242mg" "ICBIM_22028243mg" "ICBIM_22028244mg" "ICBIM_22028245mg" "ICBIM_22028246mg" "ICBIM_22028247mg"

read.fwf(textConnection(annotations$X9), widths = c(50, 16), stringsAsFactors = FALSE)[, 2]
# [1] "ICBIM_22028242mg" "ICBIM_22028243mg" "ICBIM_22028244mg" "ICBIM_22028245mg" "ICBIM_22028246mg" "ICBIM_22028247mg"

提取特定词

Extract specific word

regex

r

bioinformatics