从 R 中的长字符串中提取 substring
[英]extract substring from a long string in R
问题描述
I have a string that looks like this:
我有一个看起来像这样的字符串：
C|3_prime_UTR_variant|MODIFIER|SRY|ENSG00000184895|Transcript|ENST00000383070|protein_coding|1/1||ENST00000383070.1:c.*51C>G||762|||||rs781744002|1||-1||SNV|1|HGNC|11311|YES|||CCDS14772.1|ENSP00000372547|Q05066|Q6J4J1&A7WPU8|UPI0000135F78|1||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|upstream_gene_variant|MODIFIER|RNASEH2CP1|ENSG00000237659|Transcript|ENST00000454281|processed_pseudogene||||||||||rs781744002|1|2889|1||SNV|1|HGNC|24117|YES||||||||||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|downstream_gene_variant|MODIFIER|RNU6-1334P|ENSG00000251841|Transcript|ENST00000516032|snRNA||||||||||rs781744002|1|2085|1||SNV|1|HGNC|48297|YES||||||||||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|downstream_gene_variant|MODIFIER|SRY|ENSG00000184895|Transcript|ENST00000525526|protein_coding||||||||||rs781744002|1|70|-1||SNV|1|HGNC|11311|||||ENSP00000437575||F5H6J8|UPI0002064E1A|1||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|downstream_gene_variant|MODIFIER|SRY|ENSG00000184895|Transcript|ENST00000534739|protein_coding||||||||||rs781744002|1|166|-1||SNV|1|HGNC|11311|||||ENSP00000438917||F5H3H1|UPI0002064E1B|1||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||"
what I wish to do is to extract from the string the data that is bold我想做的是从字符串中提取粗体数据
C| C| 3_prime_UTR_variant |MODIFIER| 3_prime_UTR_variant |修改器| SRY |ENSG00000184895|Transcript|ENST00000383070|protein_coding|1/1||ENST00000383070.1:c.*51C>G||762|||||rs781744002|1||-1||SNV|1|HGNC|11311|YES|||CCDS14772.1|ENSP00000372547|Q05066|Q6J4J1&A7WPU8|UPI0000135F78|1||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|upstream_gene_variant|MODIFIER|RNASEH2CP1|ENSG00000237659|Transcript|ENST00000454281|processed_pseudogene||||||||||rs781744002|1|2889|1||SNV|1|HGNC| SRY |ENSG00000184895|成绩单|ENST00000383070|protein_coding|1/1||ENST00000383070.1:c.*51C>G||762|||||rs781744002|1||-1||SNV|1|HGNC|11311|是|||CCDS14772.1|ENSP00000372547|Q05066|Q6J4J1&A7WPU8|UPI0000135F78|1||||||C:0|||||||C:0|C:2.855e-05|C:0|C :3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|upstream_gene_variant|MODIFIER|RNASEH2CP1|ENSG00000237659|Transcript|ENST00000454281 |processed_pseudogene||||||||||rs781744002|1|2889|1||SNV|1|HGNC| 24117 |YES||||||||||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|downstream_gene_variant|MODIFIER|RNU6-1334P|ENSG00000251841|Transcript|ENST00000516032|snRNA||||||||||rs781744002|1|2085|1||SNV|1|HGNC|48297|YES||||||||||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|downstream_gene_variant|MODIFIER|SRY|ENSG00000184895|Transcript|ENST00000525526|protein_coding||||||||||rs781744002|1|70|-1||SNV|1|HGNC|11311|||||ENSP00000437575||F5H6J8|UPI0002064E1A|1||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|downstream_gene_variant|MODIFIER|SRY|ENSG00000184895|Transcript|ENST00000534739|protein_coding||||||||||rs781744002|1|166|-1||SNV|1|HGNC|11311|||||ENSP00000438917||F5H3H1|UPI0002064E1B|1||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||" 24117 |是|||||||||||||C:0|||||||C:0|C:2.855e-05|C:0|C:3.067e-05| C:0|C:0|C:5.473e-05|C:0||||||||||||,C|downstream_gene_variant|修饰符|RNU6-1334P|ENSG00000251841|转录本|ENST00000516032|snRNA|| ||||||||rs781744002|1|2085|1||SNV|1|HGNC|48297|是|||||||||||||C:0||||||| |C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||| |||,C|downstream_gene_variant|MODIFIER|SRY|ENSG00000184895|转录本|ENST00000525526|protein_coding|||||||||rs781744002|1|70|-1||SNV|1|HGNC|11311|||| |ENSP00000437575||F5H6J8|UPI0002064E1A|1||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C: 0|C:0|C:5.473e-05|C:0||||||||||||,C|downstream_gene_variant|MODIFIER|SRY|ENSG00000184895|Transcript|ENST00000534739|protein_coding|||||| ||||rs781744002|1|166|-1||SNV|1|HGNC|11311|||||ENSP00000438917||F5H3H1|UPI0002064E1B|1|||||C:0||||||| |C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||| |||”
usually, i use this type of code:通常，我使用这种类型的代码：
str_extract(data_snp$vep, "(?<=xxx=)[^|]+")
but this time it didn't work.但是这次没有用。 Is there any way that R can do this? R 有什么办法可以做到这一点吗？ thank you:)谢谢你：）
3 个解决方案
解决方案1
3 已采纳 2022-12-27 14:58:24
We can use read.delim for this:我们可以为此使用read.delim ：
txt <- "C|3_prime_UTR_variant|MODIFIER|SRY|ENSG00000184895|Transcript|ENST00000383070|protein_coding|1/1||ENST00000383070.1:c.*51C>G||762|||||rs781744002|1||-1||SNV|1|HGNC|11311|YES|||CCDS14772.1|ENSP00000372547|Q05066|Q6J4J1&A7WPU8|UPI0000135F78|1||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|upstream_gene_variant|MODIFIER|RNASEH2CP1|ENSG00000237659|Transcript|ENST00000454281|processed_pseudogene||||||||||rs781744002|1|2889|1||SNV|1|HGNC|24117|YES||||||||||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|downstream_gene_variant|MODIFIER|RNU6-1334P|ENSG00000251841|Transcript|ENST00000516032|snRNA||||||||||rs781744002|1|2085|1||SNV|1|HGNC|48297|YES||||||||||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|downstream_gene_variant|MODIFIER|SRY|ENSG00000184895|Transcript|ENST00000525526|protein_coding||||||||||rs781744002|1|70|-1||SNV|1|HGNC|11311|||||ENSP00000437575||F5H6J8|UPI0002064E1A|1||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||,C|downstream_gene_variant|MODIFIER|SRY|ENSG00000184895|Transcript|ENST00000534739|protein_coding||||||||||rs781744002|1|166|-1||SNV|1|HGNC|11311|||||ENSP00000438917||F5H3H1|UPI0002064E1B|1||||||C:0||||||||C:0|C:2.855e-05|C:0|C:3.067e-05|C:0|C:0|C:5.473e-05|C:0||||||||||||"
unlist(read.delim(text = txt, sep = "|", header = FALSE)[,c(2,4,93)], use.names = FALSE)
# [1] "3_prime_UTR_variant" "SRY" "24117"
If you use unlist(.) without use.names=FALSE , you get V1 etc for names, but they are harmless.如果您在不使用use.names=FALSE的情况下使用unlist(.) ，您将获得V1等名称，但它们是无害的。
解决方案2
0 2022-12-27 15:10:03
One possible way to solve your problem:解决问题的一种可能方法：
lapply(strsplit(data_snp$vep, "\\|+"), \(x) intersect(x, c("3_prime_UTR_variant", "SRY", "24117")))
[[1]]
[1] "3_prime_UTR_variant" "SRY" "24117"
解决方案3
0 2022-12-27 15:23:06
You can use strsplit() :您可以使用strsplit() ：
strsplit(txt, '\\|')[[1]][c(2, 4, 93)]
# [1] "3_prime_UTR_variant" "SRY" "24117"
or stringr::word() :或stringr::word() ：
stringr::word(txt, c(2, 4, 93), sep = '\\|')
# [1] "3_prime_UTR_variant" "SRY" "24117"
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