Printing Reverse Complement Of Dna In Single-Line Perl
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11.2 years ago
soosus ▴ 90

I want to write a quick single-line perl script to produce the reverse complement of a sequence of DNA. The following isn't working for me, however:

$ cat sample.dna.sequence.txt | perl -ne '{while (<>) {$seq = $_; $seq =~ tr /atcgATCG/tagcTAGC/; $revComp = reverse($seq); print $revComp;}}'

Any suggestions?

perl bash sequence • 17k views
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The simpler version is: cat test.txt | perl -pe 'chomp;tr/ACGTacgt/TGCAtgca/;$_=reverse."\n"'

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an even simpler version is cat test.txt | perl -pe 'tr/ACGTacgt/TGCAtgca/;reverse'

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8.7 years ago
Shicheng Guo ★ 9.5k

Why use single line. keep the code to your script fold and use these routine script everyday.

Like: perl /home/usr/bin/rcdna.pl ATCGATGCG

#!/usr/bin/perl
use strict;
my $dna=shift @ARGV;
my $rcdna= & reverse_complement_IUPAC($dna);
print "$rcdna\n";

sub reverse_complement_IUPAC {
        my $dna = shift;

        # reverse the DNA sequence
        my $revcomp = reverse($dna);

        # complement the reversed DNA sequence
        $revcomp =~ tr/ABCDGHMNRSTUVWXYabcdghmnrstuvwxy/TVGHCDKNYSAABWXRtvghcdknysaabwxr/;
        return $revcomp;
}
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5
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11.2 years ago

shell script? you don't need perl:

tr -d "\n " < input.txt | tr "[ATGCatgcNn]" "[TACGtacgNn]" | rev
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Here is the modified solution that can handle IUPAC degeneracies:

tr -d "\n" < input.txt | tr "[ATGCUatgcuNnYyRrSsWwKkMmBbDdHhVv]" "[TACGAtacgaNnRrYySsWwMmKkVvHhDdBb]" | rev
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Say I want to do it with perl, for illustrative purposes. How do I go about that? And why doesn't my code work?

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you need to concatenate all the strings in the while lool. Once everything is read, call tr , reverse and print.

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11.2 years ago

If you want to use Perl:

$ echo "CAAT" | perl -le '{$seq = <STDIN>; chomp $seq; $seq =~ tr /atcgATCG/tagcTAGC/; $seq = reverse($seq); print $seq; }'
ATTG

STDIN is a default handle, so you could just take that out for brevity. I like being explicit if it isn't too wordy, though.

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for this matter I usually go for this compact yet self-explanatory code inside my scripts

echo -n "CAAT" | perl -pe '{tr/atcgATCG/tagcTAGC/; $_=reverse}'

although I would agree that if reverse complementing is the only thing you want to do, you'll probably find shell scripting faster.

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11.2 years ago
Asaf 10k

This will give you the reverse complement of each line, try something like:

$tail -n +2 seq.fa | tr -d "\n" |tr "acgtACGT" "tgcaTGCA" |rev
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11.2 years ago
soosus ▴ 90
perl -0777pe's/\n //g; tr/ATGCatgcNn/TACGtacgNn/; $_ = reverse $_;' sample.sequence.txt
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8.3 years ago
winter_li ▴ 60

Hi , maybe you can write a perl script like the following ,

  use Bio::Seq;

  $seqobj = Bio::Seq->new(-seq => $seq);
  $Query = $seqobj->revcom()->seq;

Good luck !

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