Use of the Rename Command

Question

I have a two part question.

I have a series of files with the names "file.pdb.#", where # is an integer.

1.) How can I script to rename all the "file.pdb.#" to "file_#.pdb", where the integer is preserved? All files are in the same directory.

I presumably need to read in the constant string (file.pdb.) with the variable being the #.

2.) Even more important, how would I have searched for this answer, properly, among answered questions? I have no doubt this question has been answered many times before. However, I am not sure how I might have properly searched for the answer to this question (and obviously I should learn to search previously answered questions better to not bother people in the future). I cannot imagine what the right search string is (googling how to read in files and rename them in Linux is awfully generic and I waded through suggestions not germane to this sort of file format manipulation).

Answer 1

You can use capture groups and backreferences e.g.

rename -vn -- 's/\.(pdb)\.(\d+)/_$2.$1/' *.pdb.*

to match a literal period \. followed by (literal) string pdb, followed by a second period \. and then a sequence of one or more digits \d+, copying the string and digit sequence into numbered capture groups $1 and $2 respectively and then re-substituting them in reverse order with an underscore in place of the first period.

Options -v and -n are for verbose output (listing any changes made) and no-operation, allowing you to test the correctness before committing to making any actual substitutions: you will need to remove the n option to actually apply the changes.

The -- marks the end of command options - this just makes the command more robust in the rare case that you have filenames that start with a hyphen.

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Testing it in a directory containing files file.pdb.1 file.pdb.2 file.pdb.3 file.pdb.4 file.pdb.5 (among others):

$ rename -vn -- 's/\.(pdb)\.(\d+)/_$2.$1/' *.pdb.*
file.pdb.1 renamed as file_1.pdb
file.pdb.2 renamed as file_2.pdb
file.pdb.3 renamed as file_3.pdb
file.pdb.4 renamed as file_4.pdb
file.pdb.5 renamed as file_5.pdb

Answer 2

The strictest way possible, so that only filenames starting with file.pdb. followed by at least a digit will be renamed, using rename:

rename -n 's/(file)(\.pdb)\.([0-9]+)/$1_$3$2/' *

If the result is the expected one, remove the -n option:

rename 's/(file)(\.pdb)\.([0-9]+)/$1_$3$2/' *

Answer 3

Apart from excellent rename answers you have received already, you can use bash parameter expansion:

for i in *.pdb.*; do mv -i "$i" "${i%%.pdb.*}_${i##*.}.pdb"; done

• The pattern ${i%%.pdb*} will get the file portion of name file.pdb.#

• ${i##*.} will get the digits after .pdb.