rename a bunch of files with bash by regular expression

I am at the MSU NGS 2014 course. My colleague wanted to follow the khmer protocol with his own data, but one of the steps has to use a certain file name convention.

In the protocol it requires fastq files listed as:   *001_R1.fastq.gz

001 is the replicate number, it can be 002 or 003 or any number of replicates you have. ( for RNA-seq, sequence as many as biological samples as possible !)

R1 is the pair-end reads 1, it can be R2

What he has is something like:

1_egg_r1_01_sub.fastq.gz

1 is the stage of the egg. He sequenced  4 eggs, so he has 1_egg, 2_egg., 3_egg and 4_egg

r1 is the pair-end reads 1

01 is the first replicates. He has two replicates for each egg.

Basically, he wants to rename these files to the khmer convention.

This problem gets down to writing a regular expression.

To recapture the problem, I made some dummy files:

mkdir foo && cd foo

I have a txt file contains the names of the file:

foo$ cat files.txt 

1egg_r1_01_sub.fastq.gz

1egg_r2_01_sub.fastq.gz

1egg_r1_02_sub.fastq.gz

1egg_r2_02_sub.fastq.gz

2egg_r1_01_sub.fastq.gz

2egg_r2_01_sub.fastq.gz

2egg_r1_02_sub.fastq.gz

2egg_r2_02_sub.fastq.gz

3egg_r1_01_sub.fastq.gz

3egg_r2_01_sub.fastq.gz

3egg_r1_02_sub.fastq.gz

3egg_r2_02_sub.fastq.gz

4egg_r1_01_sub.fastq.gz

4egg_r2_01_sub.fastq.gz

4egg_r1_02_sub.fastq.gz

4egg_r2_02_sub.fastq.gz

Now I want to make dummy files with the names in this file.

one can make the dummy files in a fly also.

=====update on 08/26/14======
one can use the {} expansion to create the dummy files

tommy@tommy-ThinkPad-T420[foo] touch {1,2,3,4}_r{1,2}_0{1,2}_sub.fastq.gz
tommy@tommy-ThinkPad-T420[foo] ls                                     [ 3:45PM]
1_r1_01_sub.fastq.gz  2_r2_01_sub.fastq.gz  4_r1_01_sub.fastq.gz
1_r1_02_sub.fastq.gz  2_r2_02_sub.fastq.gz  4_r1_02_sub.fastq.gz
1_r2_01_sub.fastq.gz  3_r1_01_sub.fastq.gz  4_r2_01_sub.fastq.gz
1_r2_02_sub.fastq.gz  3_r1_02_sub.fastq.gz  4_r2_02_sub.fastq.gz
2_r1_01_sub.fastq.gz  3_r2_01_sub.fastq.gz
2_r1_02_sub.fastq.gz  3_r2_02_sub.fastq.gz

========================

The difference of make_dummy_file.sh and make_dummy_file_1.sh is that I specified shebang line in the make_dummy_file.sh script to tell the bash that it is a bash script, to invoke it: ./make_dummy_file.sh files.txt

In contrast, to invoke the other two which I did not specify the shebang: bash make_dummy_file_1.sh bash make_dummy_file_2.sh

Rename the files with regular expression by either using sed or rename command

the rename command use the perl regular expression. use \ to escape $.
the sed command need to escape the () which are used to capture the back reference
before:
tommy@tommy-ThinkPad-T420:~/foo$ ls 1_egg_r1_01_sub.fastq.gz 2_egg_r1_01_sub.fastq.gz 3_egg_r1_01_sub.fastq.gz 4_egg_r1_01_sub.fastq.gz copy make_dummy_file_1.sh 1_egg_r1_02_sub.fastq.gz 2_egg_r1_02_sub.fastq.gz 3_egg_r1_02_sub.fastq.gz 4_egg_r1_02_sub.fastq.gz dummy make_dummy_file_2.sh 1_egg_r2_01_sub.fastq.gz 2_egg_r2_01_sub.fastq.gz 3_egg_r2_01_sub.fastq.gz 4_egg_r2_01_sub.fastq.gz files.txt rename.sh 1_egg_r2_02_sub.fastq.gz 2_egg_r2_02_sub.fastq.gz 3_egg_r2_02_sub.fastq.gz 4_egg_r2_02_sub.fastq.gz make_dummy_file.sh rename_one_liner.sh 

after:
tommy@tommy-ThinkPad-T420:~/foo$ ls 1egg_R1_001.fastq.gz 2egg_R1_001.fastq.gz 3egg_R1_001.fastq.gz 4egg_R1_001.fastq.gz copy make_dummy_file_1.sh 1egg_R1_002.fastq.gz 2egg_R1_002.fastq.gz 3egg_R1_002.fastq.gz 4egg_R1_002.fastq.gz dummy make_dummy_file_2.sh 1egg_R2_001.fastq.gz 2egg_R2_001.fastq.gz 3egg_R2_001.fastq.gz 4egg_R2_001.fastq.gz files.txt rename.sh 1egg_R2_002.fastq.gz 2egg_R2_002.fastq.gz 3egg_R2_002.fastq.gz 4egg_R2_002.fastq.gz make_dummy_file.sh rename_one_liner.sh

References: http://stackoverflow.com/questions/399078/what-special-characters-must-be-escaped-in-regular-expressions

http://stackoverflow.com/questions/10929453/bash-scripting-read-file-line-by-line
https://www.cs.tut.fi/~jkorpela/perl/regexp.html