How to match multi-row data using regular expression R programming

Question

I import a txt document into R using readLines, but the document is transformed into a charactor vector, namely,every element in the vector denote a line in the txt document, so that I cannot use regular expression to match the multi-row data.How to sove this problem?

example document test.txt

ID   cel-let-7         standard; RNA; CEL; 99 BP.

XX

AC   MI0000001;

XX
DE   Caenorhabditis elegans let-7 stem-loop

XX

RN   [1]

RX   PUBMED; 11679671.

RA   Lau NC, Lim LP, Weinstein EG, Bartel DP;

RT   "An abundant class of tiny RNAs with probable regulatory roles in

RT   Caenorhabditis elegans";

RL   Science. 294:858-862(2001).

I need the data between ID and DE,but the code below don't work, because no way to match multi-row.

pattern <- 'ID.+\nXX\nAC.+\nXX')
m <- gregexpr(pattern, text, perl = T)  

perhaps there has another method but I only want to solve using regular expression.

Answer 1

The below command would fetch the lines between ID and DE

> f <- paste(readLines("file"), collapse="\n")
> m <- gregexpr("(?m)^ID.*\\n\\K[\\S\\s]*?(?=\\nDE)", f, perl=TRUE)
> regmatches(f, m)
[[1]]
[1] "\nXX\n\nAC   MI0000001;\n\nXX"

OR

> m <- gregexpr("(?s)^ID.*?\\nDE", f, perl=TRUE)
> regmatches(f, m)
[[1]]
[1] "ID   cel-let-7         standard; RNA; CEL; 99 BP.\n\nXX\n\nAC   MI0000001;\n\nXX\nDE"