Regular expression in rename Unix command

user_16844588 0
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I am trying to rename some files and am pretty new to regular expressions. I know how to do this the long way, but I am trying some code golf to shorten it up.

My file:

abc4800_12_S200_R1_001.fastq.gz

My goal:

abc4800_12_R1.fastq.gz

Right now I have a two-step process for renaming it:

rename 's/_S[0-9]+//g' *gz
rename 's/_001//g' *gz

But I was trying to shorten this into one single line to clean it up in one go.

I was trying to use a regular expression to skip over the parts in between, but I don’t know if that is actually a possibility in this function.

rename 's/_S[0-9]+_*?_001//g' *gz
rename unix regex
3 Answers

Use a capture group to preserve the middle part of the segment you're replacing.

rename 's/_S\d+_(.*)_001/_$1/' *gz
user_14918950

With your shown samples, please try the following rename command. I am using the -n option here which is a dry run for command. Once you are happy with the output (like how files are going to rename if we run actual code), remove the -n option from the following rename code.

rename -n 's/(^[^_]*_[^_]*)_[^_]*(_[^_]*)[^.]*(\..*$)/$1$2$3/' *.gz

The output will be as follows:

rename(abc4800_12_S200_R1_001.fastq.gz, abc4800_12_R1.fastq.gz)

Explanation:

(^[^_]*_[^_]*)  ## Creating the 1st capturing group which captures everything from starting to just before 2nd occurrence of _ here.
_[^_]*          ## Matching (without a capturing group) _ then just before the next occurrence of _ here.
(_[^_]*)        ## Creating the 2nd capturing group here which matches _, followed by before the next occurrence of _ here.
[^.]*           ## Matching everything just before dot comes (not capturing here).
(\..*$)         ## Creating the 3rd capturing group which has a dot till the end of line in it.
user_58665800

You are trying to replace two parts in the string with nothing. Use the alternation operator. It will match the left or the right side; replacing any match with the same replacement string (i.e. nothing):

rename 's/_S[0-9]+|_001//g' *gz
user_1129680
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