In <1992Sep10.165929.3773 at magnus.acs.ohio-state.edu> gchacko at magnus.acs.ohio-state.edu (George W Chacko) writes:
>I need to generate the reverse complement of a DNA sequence on a Unix
>machine. Transferring the file to a VAx and using GCG is laborious.
Try the following 'one-liner':
tail -r INPUTFILE | rev | tr atgcATGC tacgTACG > OUTPUTFILE
It should do what you ask. Your input file must contain DNA sequence only,
comment lines beginning with '>' are NOT ignored and will be read as sequence.
I could probably find a way to handle that if required.
If you want to put this into a script file try:
if test $1
tail -r $1 | rev | tr atgcATGC tacgTACG >$1.rev
echo "usage: $0 <dna_sequence_file>"
Make the file executable with the command 'chmod 755 script-flie'. It will
produce an output file with the extension .rev when called from the
command line, e.g. revcomp humtnfa ==produces==> humtnfa.rev
I'm currently working on some other unix scripts for simple sequence
manipulation based on traditional unix commands. Does anyone have
any suggestions? ...dare I ask!
Mario Pinelli (pinelli at murdoch.edu.au)
Murdoch, W.A., 6150,