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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?

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.

genome sequence
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updated by Ram Ram • written by Sumit • Sumit

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

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written by Whetting Whetting

1 answer 

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

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

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updated by Ram Ram • written by Biomonika (Noolean) Biomonika (Noolean)

Alternatively (-l60 to specify fasta line length):

ls *.fasta | sed s,.fasta,, | xargs -i echo seqtk seq -r -l60 {}.fasta \> {}.rev | sh
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updated by Ram Ram • written by lh3 lh3

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

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written by Sumit • Sumit

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