Rename and move Spades assemblies in batch

Question

[jellila]

Hi.

I have a folder called "spades" with many subdirectories generated by Spades (each with the name of the sequenced strain). I would like to rename the "contigs.fasta" file with the name of the folder (for ex. DI21.fasta that is in the "DI21" folder) and move the renamed fasta file to a different directory where I want to collect all the fasta files of the different strains. How can i do it in batch? I am working in bash on a mac.

Thank you.

Laura

Answer 1

[Asaf]

I guess you can use a bash script to do that. Something like:

for f in */contigs.fasta; do cp $f /destination/dir/${f%/contigs.fasta}.fasta; done

The % removes the following text from the variable so the contigs.fasta will be changed to the folder name.

(I didn't test it but it should work)

[jellila]

This worked perfectly, thank you very much Asaf!! :)