How to find out the reverse complement of DNA from each FASTA formated sequence file in a directory and generate a new reverse complement FASTA formated files for each of the input files?

Question

[Sumit]

I have total 2000+ genome sequence files in a directory. I need reverse complement sequence for each of the files and want to generate FASTA formated reverse complement sequence file for each files in the directory.

[Whetting]

Hi, welcome to Biostars. Look into Biopython, Bioperl etc.

Answer 1

[Biomonika (Noolean)]

for file in *.fasta; do seqtk seq -r ${file} > ${file}_revC; done;

not tested, should work, please install seqtk: https://github.com/lh3/seqtk

[lh3]

Alternatively (-l60 to specify fasta line length):

ls *.fasta | sed s,.fasta,, | xargs -i echo seqtk seq -r -l60 {}.fasta \> {}.rev | sh

[Sumit]

I am grateful to you for your help.. Its work....