CODEWITHSUNDEEP
rregex
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Reputation: 715

How to extract text from a string using a regular expression in R?

I have a vector of strings such as:

x <- c("gene_biotype \"protein_coding\"; transcript_name \"IGHV3-66-201\"; 
transcript_source \"havana\"; transcript_biotype \"IG_V_gene\"; 
protein_id \"ENSP00000375041\"; protein_version \"2\"; tag 
\"cds_end_NF\"; tag \"mRNA_end_NF\"; tag \"basic\"; 
transcript_support_level \"NA\";",
"gene_id \"ENSG00000211973\"; gene_version \"2\"; transcript_id 
\"ENST00000390633\"; transcript_version \"2\"; exon_number \"1\"; 
gene_name \"IGHV1-69\"; gene_source \"ensembl_havana\"; gene_biotype 
\"IG_V_gene\"; transcript_name \"IGHV1-69-201\"; transcript_source 
\"ensembl_havana\"; transcript_biotype \"IG_V_gene\"; protein_id 
\"ENSP00000375042\"; protein_version \"2\"; tag \"cds_end_NF\"; tag 
\"mRNA_end_NF\"; tag \"basic\"; transcript_support_level \"NA\";",
"gene_id \"ENSG00000211973\"; gene_version \"2\"; transcript_id 
\"ENST00000390633\"; transcript_version \"2\"; exon_number \"2\"; 
gene_name \"IGHV1-69\"; gene_source \"ensembl_havana\"; gene_biotype 
\"protein_coding\";")

I need to extract the quoted text (any characters) that follows gene_biotype. For example:

[1] protein_coding\ 
[2] IG_V_gene\
[3] protein_coding\

I have tried using str_extract in the stringr package, but I cannot get the regex to work.

Any help would be greatly appreciated!

Upvotes: 1

Views: 75

Answers (2)

MarBlo
MarBlo

Reputation: 4534

I found this here

stringi::stri_extract_all_regex(x, '(?<=").*?(?=")')[[1]][1]
#[1] "protein_coding"

Upvotes: -1

MrFlick
MrFlick

Reputation: 206576

You can use a regular expression with some help from the stringr package to get the data you need. For example

library(stringr)
str_match(x, "gene_biotype\\s+\"([^\"]+)\"")
#      [,1]                                [,2]            
# [1,] "gene_biotype \"protein_coding\""   "protein_coding"
# [2,] "gene_biotype \n\"IG_V_gene\""      "IG_V_gene"     
# [3,] "gene_biotype \n\"protein_coding\"" "protein_coding"

This returns a matrix with the match and the category. If you just want the category you can do

str_match(x, "gene_biotype\\s+\"([^\"]+)\"")[,2]
# [1] "protein_coding" "IG_V_gene"      "protein_coding"

Upvotes: 4

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