Starting with a tab separated fileUse the reverse utility and sed to generate the reverse complement of a tabulated sequence file.
cut -f2 file | rev | sed 'y/CGAT/GCTA/'
You could also make the reverse complemented sequence in lower case using sed 'y/CGAT/gcta/'
If you need the sequence name, paste it back.
cut -f2 file | rev | sed 'y/CGAT/GCTA/' | paste file -
Starting with a fastaNow starting with a fasta file. Avoid tabs and special characters in the sequence name.
paste - - < file > tmp
cut -f2 tmp | rev | sed 'y/CGAT/GCTA/' \
| paste tmp - | cut -f1,3 | tr '\t' '\n'