[SOLVED] How to replace a character using sed with different lengths in preceding string

Issue

I have a file in which I want to replace the "_" string with "-" in cases where it makes up a part of my gene name. Examples of the gene names and my intended output are:

aa1c1_123 -> aa1c1-123
aa1c2_456 -> aa1c1-456
aa1c10_789 -> aa1c1-789

In essence, the first four characters are fixed, followed by 1 or 2 characters depending on the chromosome, an underscore and then the remainder of the gene ID which could vary in length and character. Important is that there are other strings in this gene information column contains other strings with underscores (e.g. "gene_id", "transcript_id", "five_prime_utr") so using sed -i.bak s/_/-/g' file.gtf can't be done.

Solution

Perhaps not the most elegant way, but this should work:

sed -i.bak 's/\([0-9a-z]\{4\}[0-9][0-9]\?\)_/\1-/g' file.gtf

i.e. capture a group (referenced by \1 in the substitution) of 4 characters consisting of lower case letters and digits followed by exactly one digit and perhaps another digit, which is followed by an underscore; if found, replace it by the group's content and a dash. This should exclude your other occurrences consisting of only characters and an underscore.

Answered By - Else Ifthen

Answer Checked By - Cary Denson (WPSolving Admin)