Question: Use UNIX reverse complement
0
gravatar for avranarkin
29 days ago by
avranarkin0
avranarkin0 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 • 183 views
ADD COMMENTlink modified 29 days ago by Alex Reynolds21k • written 29 days ago by avranarkin0

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 29 days ago • written 29 days ago by Michael Dondrup43k
4
gravatar for Alex Reynolds
29 days ago by
Alex Reynolds21k
Seattle, WA USA
Alex Reynolds21k 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 25 days ago • written 29 days ago by Alex Reynolds21k
1
gravatar for James Ashmore
29 days ago by
James Ashmore2.1k
UK/Edinburgh/MRC Centre for Regenerative Medicine
James Ashmore2.1k wrote:

Install bioawk and use the following command:

bioawk -c fastx '{print ">"$name;print revcomp($seq)}' seq.fa.gz
ADD COMMENTlink written 29 days ago by James Ashmore2.1k

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

ADD REPLYlink written 29 days ago by avranarkin0
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