Question

I have a long file which is written as ONLY one column.
This column contains gene names followed by a colon (:) then by the name of a microRNA fragment.
Unfortunately, the microRNA name MAY ALSO contain a colon (:).

I want to replace ONLY the first colon with a tab (\t) and then write.table to produce two columns in R.

Here is a representative sample of one gene name with multiple microRNAs:

CHD5:miR-329/362-3p:2
CHD5:miR-329/362-3p:1
CHD5:miR-30a/30a-5p/30b/30b-5p/30cde/384-5p
CHD5:miR-15/16/195/424/497
CHD5:miR-26ab/1297
CHD5:miR-17-5p/20/93.mr/106/519.d
CHD5:miR-130/301
CHD5:miR-19
CHD5:miR-204/211

Any suggestions?

Answer 1

Here’s a slightly more complete example if you have your ‘inFile’ and want ‘outFile’…

lines <- readLines('inFile')
lines <- sub(':', '\t', x)
writeLines(lines, 'outFile')