Question: Use UNIX reverse complement
1
gravatar for avranarkin
12 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 • 883 views
ADD COMMENTlink modified 12 months ago by Alex Reynolds26k • written 12 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 12 months ago • written 12 months ago by Michael Dondrup44k
5
gravatar for Alex Reynolds
12 months ago by
Alex Reynolds26k
Seattle, WA USA
Alex Reynolds26k 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 12 months ago • written 12 months ago by Alex Reynolds26k
1
gravatar for James Ashmore
12 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 12 months ago by James Ashmore2.5k

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

ADD REPLYlink written 12 months ago by avranarkin10
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