Question: Use UNIX reverse complement
1
gravatar for avranarkin
10 months ago by
avranarkin10
avranarkin10 wrote:

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 • 656 views
ADD COMMENTlink modified 10 months ago by Alex Reynolds24k • written 10 months ago by avranarkin10

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.

ADD REPLYlink modified 10 months ago • written 10 months ago by Michael Dondrup44k
5
gravatar for Alex Reynolds
10 months ago by
Alex Reynolds24k
Seattle, WA USA
Alex Reynolds24k wrote:
$ 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

ADD COMMENTlink modified 9 months ago • written 10 months ago by Alex Reynolds24k
1
gravatar for James Ashmore
10 months ago by
James Ashmore2.5k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.5k wrote:

Install bioawk and use the following command:

bioawk -c fastx '{print ">"$name;print revcomp($seq)}' seq.fa.gz
ADD COMMENTlink written 10 months ago by James Ashmore2.5k

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

ADD REPLYlink written 10 months ago by avranarkin10
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