Batch Renaming of Files in Linux Shell

Question

I am working via ssh on a remote cluster and need to rename some files according to a scheme. The rename should work like:

M-19-3778_P1-DX5-K47-232-Elev_A1-A1_L001_R1_001.fastq.gz into
M-19-3778-P1-DX5-K47-232-Elev-A1-A1L001_R1.R.fq.gz

M-19-3778_P1-DX5-K47-232-Elev_A1-A1_L001_R2_001.fastq.gz into
M-19-3778-P1-DX5-K47-232-Elev-A1-A1L001_R1.F.fq.gz

M-19-3779_P1-F48-F37-86-Cont_A2-A2_L001_R1_001.fastq.gz into
M-19-3779-P1-F48-F37-86-Cont-A2-A2L001_R2.R.fq.gz

M-19-3779_P1-F48-F37-86-Cont_A2-A2_L001_R2_001.fastq.gz into
M-19-3779-P1-F48-F37-86-Cont-A2-A2L001_R2.F.fq.gz

...

M-19-3830_P1-DX5-D12-221-Elev_F9-F9_L001_R1_001.fastq.gz into
M-19-3830-P1-DX5-D12-221-Elev-F9-F9L001_R53.R.fq.gz

M-19-3830_P1-DX5-D12-221-Elev_F9-F9_L001_R2_001.fastq.gz into
M-19-3830-P1-DX5-D12-221-Elev-F9-F9L001_R53.F.fq.gz

Iterations are only in the beginning of the names with 3778....

So far I've tried it with combinations of grep / sed / cat but did not succeed. And I have no idea how to handle the iteration in the end of the name R1 , R2 ,..., my guess would be a combination of a for loop and an if -Statement but I just don't get this running.

I would be grateful for any help!

Answer 1

i=1
for name in *
do
    newName=${name%_L001_R1_001.fastq.gz}L001_R$i.R.fq.gz
    mv "$name" "$oldname"
    ((i++))
done