Change the field separator

Question

[ATCG]

Hi, I have the following character:

CG10226/CG33120/RyR/Tsp42Eg/CG1234/Act57B/Apoltp/CG9194

and need to change the field separator from "/ " to "," so that my character will look like this:

CG10226,CG33120,RyR,Tsp42Eg,CG1234,Act57B,Apoltp,CG9194

Thanks in advance for your help!

Answer 1

[Quentin M]

In R :

library("stringr")   
str_replace_all(string = "CG10226/CG33120/RyR/Tsp42Eg/CG1234/Act57B/Apoltp/CG9194", pattern = "/", replacement = ",")

[ATpoint]

Without any additional package:

gsub("/",",","CG10226/CG33120/RyR/Tsp42Eg/CG1234/Act57B/Apoltp/CG9194")

Answer 2

[Pierre Lindenbaum]

depends of the context :

use awk+gsub https://www.gnu.org/software/gawk/manual/html_node/String-Functions.html if it's a token among multiple columns.

just use tr if it's the whole line.

Answer 3

[Jeffin Rockey]

sed 's|\/|,|g'

[ATCG]

Hi Jeffin, Thanks for your answer. Can you be more specific please?

[Jeffin Rockey]

sed is a very handy utility which would be there is many of the unix/linux flavours.

s stands for substitute.

The | (pipes) act as separators. And it need not be | always. You may as well write like sed 's/\//,/g' (I am pretty sure it would confuse more, and hence the pipes)

\/ kind of says to look for / and just treat it as a character and do not mean any further meanings to it.

, is the replacement.

g indicates globally

In short, all this boils down to

sed, substitute a slash with a comma for all occurrences in the file.

You may use it like

sed 's|\/|,|g' file.txt >file.comma.sep.txt
or
sed <file.txt  's|\/|,|g'  >file.comma.sep.txt
or
echo "the/slash/separated/string" | sed 's|\/|,|g'

The above will write the output after replacement to the new file, keeping input file intact.

If you prefer to substitute inside the input file itself rather than streaming out, use -i (be very very careful with this)

[zx8754]

Maybe read the manual for sed? https://en.wikipedia.org/wiki/Sed

Answer 4

[zx8754]

Using R, just read the file with sep:

read.table("myFile.txt", sep = "/")
#       V1      V2  V3      V4     V5     V6     V7     V8
#1 CG10226 CG33120 RyR Tsp42Eg CG1234 Act57B Apoltp CG9194