Use UNIX reverse complement

Question

[avranarkin]

I have downloaded the FASTA DNA sequence, how to use UNIX to reverse complement each line of the file using a single line of command?

[Michael]

This looks like an assignment, what have you tried? UNIX is very diverse and not identical to GNU Linux or POSIX, which you are probably referring to.

Answer 1

[Alex Reynolds]

$ perl -pe '/^>/ ? print "\n" : chomp' test.fa | while read -r line; do if [[ "$line" == ">"* ]]; then echo $line; else tr "[ATGCatgcNn]" "[TACGtacgNn]"; fi; done | awk '{ if ($0~/^>/) { printf("%s",$0); } else { for(i=length;i!=0;i--) x=(x substr($0,i,1)) } { printf("%s\n",x); x=""; } }'

Christ, that's awful. Just take the teacher's "F" and use seqkit or something. https://github.com/shenwei356/seqkit

Answer 2

[James Ashmore]

Install bioawk and use the following command:

bioawk -c fastx '{print ">"$name;print revcomp($seq)}' seq.fa.gz

[avranarkin]

Thank you, do you know how to solve this if I just use UNIX commands?