Grep exact match with multple strings, no dash

Question

I have a list of genes like this one saved on a variable:

NOL6
NPPC
NPRL2
NRG1
NT5C1B
NUDT19
OSER1
PAEP
PARD3
PCDHA4

I want to grep all these genes at another list of the same type on a txt. I tried this:

grep -w "^$genes$" list.txt

The problem is that it returns to me genes with a dash - like this one similar to NT5C1B:

NT5C1B-RDH14

However, if I search the gene individually:

grep "^NT5C1B$" list.txt

I'll not obtain the gene with the dash but only:

NT5C1B

Is there any way to do this using grep -w or other command?

Does this answer your question? [How to make grep only match if the entire line matches?](https://stackoverflow.com/a/4709925/3832970) — Wiktor Stribiżew, Oct 16 '20 at 12:45
we need to see some text in the `list.txt` also, what is in your `$gene` variable? a single entry or all entries as you pasted in your first code block? — Kent, Oct 16 '20 at 12:46
@WiktorStribiżew I think the question was closed probably too soon... "I'll not obtain the gene with the dash but only:...." I **guess** OP wants to get `Pattern-something` in the result. Also, we didn't see the input text, we don't know if it's `-x` case. Anyway, OP didn't describe the requirement clearly. — Kent, Oct 16 '20 at 12:59

score 1 · Accepted Answer · answered Oct 16 '20 at 12:44

1

Use -x as it only selects exact matches. -w can match a string if it has non-word constituent characters after the substring. See grep(1) .

answered Oct 16 '20 at 12:44

jcnoe

1

That's it, thanks! In case there were more colums apart from the gene names like this: `chr1 NT5C1B`. Would it work? – Swimming bird Oct 16 '20 at 14:14
@Swimmingbird It will only return exact matches. So assuming you want "chr1 NT5C1B" returned, then you would need to execute `grep -x "chr1 NT5C1B"`. – jcnoe Oct 19 '20 at 14:44
And in case I only want to grep the gene name (NT5C1B)? – Swimming bird Oct 20 '20 at 17:33

1 Answers1