Remove 2nd colon and rest of the values in a dataframe using R/ Unix
3
1
Entering edit mode
5 months ago
salman_96 ▴ 50

Hi

I have a file with coordinates like this

1:834573:A:AT
1:834830:G:A
1:835092:T:G
1:842388:T:TCCGCAGGA

I want to remove second colon and everything after that, such that the file looks like this

1:834573
1:834830
1:835092
1:842388

I have tried sed but the files have uneven characters.

Kindly suggest something

coordinates SNP Unix R • 328 views
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3
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5 months ago
4galaxy77 ▴ 950

No need to use R for this - it's exactly what the cut command in unix was designed for.

❯ cat file.txt | cut -d':' -f1-2
1:834573
1:834830
1:835092
1:842388
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1
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5 months ago
awk -v OFS="\t" -F ":" '{print $1,$2}' test.txt
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1
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5 months ago
benformatics ★ 2.5k

R code that assumes your coordinates are in file test.txt. I also kept your empty spacer lines.

gsub("(\\d+\\:\\d+)\\:[AGCT]+\\:[AGCT]+","\\1",readLines('test.txt'))
[1] "1:834573" ""         "1:834830" ""         "1:835092" ""         "1:842388"

If you want to save it as a new file just wrap it with writeLines(con="new_file_name.txt") :

writeLines(gsub("(\\d+\\:\\d+)\\:[AGCT]+\\:[AGCT]+","\\1",readLines('test.txt')),con='output_test.txt')
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0
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Actually you could even simplify it to:

gsub("(\\d+\\:\\d+).*","\\1",readLines('test.txt'))
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0
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We can use ":" as delimiter, and avoid regex:

write.table(
  read.table(text = "
             1:834573:A:AT
             1:834830:G:A
             1:835092:T:G
             1:842388:T:TCCGCAGGA", sep = ":")[, 1:2],
  file = "out.txt", col.names = FALSE, row.names = FALSE, 
  quote = FALSE, sep = ":")
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