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rregexprotein-database

Extract all substrings in string

I want to extract all substrings that begin with M and are terminated by a *

The string below as an example;

vec<-c("SHVANSGYMGMTPRLGLESLLE*A*MIRVASQ")

Would ideally return;

MGMTPRLGLESLLE
MTPRLGLESLLE

I have tried the code below;

regmatches(vec, gregexpr('(?<=M).*?(?=\\*)', vec, perl=T))[[1]]

but this drops the first M and only returns the first string rather than all substrings within.

"GMTPRLGLESLLE"
Solution

  • You can use

    (?=(M[^*]*)\*)

    See the regex demo. Details:

    • (?= - start of a positive lookahead that matches a location that is immediately followed with:
    • (M[^*]*) - Group 1: M, zero or more chars other than a * char
    • \* - a * char
    • ) - end of the lookahead.

    See the R demo:

    library(stringr)
vec <- c("SHVANSGYMGMTPRLGLESLLE*A*MIRVASQ")
matches <- stringr::str_match_all(vec, "(?=(M[^*]*)\\*)")
unlist(lapply(matches, function(z) z[,2]))
## => [1] "MGMTPRLGLESLLE" "MTPRLGLESLLE"

    If you prefer a base R solution:

    vec <- c("SHVANSGYMGMTPRLGLESLLE*A*MIRVASQ")
matches <- regmatches(vec, gregexec("(?=(M[^*]*)\\*)", vec, perl=TRUE))
unlist(lapply(matches, tail, -1))
## => [1] "MGMTPRLGLESLLE" "MTPRLGLESLLE"