Rename and move Spades assemblies in batch
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
1 answer
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)
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