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Use UNIX reverse complement

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?

sequencing
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updated by Alex Reynolds Alex Reynolds • written by avranarkin • avranarkin

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.

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written by Michael Dondrup Michael Dondrup

2 answers 

$ 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

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written by Alex Reynolds Alex Reynolds

Install bioawk and use the following command:

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

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

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written by avranarkin • avranarkin

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