CODEWITHSUNDEEP
rregexgsub
BCArg
BCArg

Reputation: 2250

gsub with "|" character in R

I have a data frame with strings under a variable with the | character. What I want is to remove anything downstream of the | character.

For example, considering the string

heat-shock protein hsp70, putative | location=Ld28_v01s1:1091329-1093293(-) | length=654 | sequence_SO=chromosome | SO=protein_coding

I wish to have only:

heat-shock protein hsp70, putative

Do I need any escape character for the | character?

If I do: 

a <- c("foo_5", "bar_7")
gsub("*_.", "", a)

I get:

[1] "foo" "bar"

i.e. I am removing anything downstream of the _ character.

However, If I repeat the same task with a | instead of the _:

b <- c("foo|5", "bar|7")
gsub("*|.", "", a)

I get:

[1] "" ""

Upvotes: 0

Views: 2557

Answers (2)

Jilber Urbina
Jilber Urbina

Reputation: 61174

You have to scape | by adding \\|. Try this

> gsub("\\|.*$", "", string)
[1] "heat-shock protein hsp70, putative "

where string is

string <- "heat-shock protein hsp70, putative | location=Ld28_v01s1:1091329-1093293(-) | length=654 | sequence_SO=chromosome | SO=protein_coding"

This alternative remove the space at the end of line in the output

 gsub("\\s+\\|.*$", "", string)
[1] "heat-shock protein hsp70, putative"

Upvotes: 3

HarlandMason
HarlandMason

Reputation: 789

Maybe a better job for strsplit than for a gsub

And yes, it looks like the pipe does need to be escaped.

string <- "heat-shock protein hsp70, putative | location=Ld28_v01s1:1091329-1093293(-) | length=654 | sequence_SO=chromosome | SO=protein_coding"
strsplit(string, ' \\| ')[[1]][1]

That outputs

"heat-shock protein hsp70, putative"

Note that I'm assuming you only want the text from before the first pipe, and that you want to drop the space that separates the pipe from the piece of the string you care about.

Upvotes: 0

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