I am trying to rename some files and am pretty new to regular expression. I know how to do this the long way, but 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 regular expression to skip over the parts in between, but dont if that is actually a possibility in this function.

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

Thanks for any help

CodePudding user response：

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

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

CodePudding user response：

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

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

Output will be as follows:

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

Explanation: Adding detailed explanation for above.

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

CodePudding user response：

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