Printing reverse complement of DNA in single-line Perl - perl

Question

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? I'm aware that
tr -d "\n " < input.txt | tr "[ATGCatgcNn]" "[TACGtacgNn]" | rev
works in bash, but I want to do it with perl for the practice.

Answer 1

Your problem is that is that you're using both -n and while (<>) { }, so you end up with while (<>) { while (<>) { } }.
If you know how to do <file.txt, why did you switch to cat file.txt|?!
perl -0777ne's/\n //g; tr/ATGCatgcNn/TACGtacgNn/; print scalar reverse $_;' input.txt
or
perl -0777pe's/\n //g; tr/ATGCatgcNn/TACGtacgNn/; $_ = reverse $_;' input.txt
Or if you don't need to remove the newlines:
perl -pe'tr/ATGCatgcNn/TACGtacgNn/; $_ = reverse $_;' input.txt

Answer 2

If you need to use cat, the following one liner should work for you.
ewolf#~ $cat foo.txt
atNgNt
gatcGn
ewolf#~ $cat foo.txt | perl -ne '$seq = $_; $seq =~ tr/atcgATCG/tagcTAGC/;print reverse( $seq )'
taNcNa
ctagCn

Answer 3

Considering the DNA sequences in single-line format in a multifasta file:
cat multifasta_file.txt | while IFS= read L; do if [[ $L == >* ]]; then echo "$L"; else echo $L | rev | tr "ATGCatgc" "TACGtacg"; fi; done > output_file.txt
If your multifasta file is not in single-line format, you can transform your file to single-line before using the command above, like this:
awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' <multifasta_file.txt >multifasta_file_singleline.txt<="" p="">
Then,
cat multifasta_file_SingleLine.txt | while IFS= read L; do if [[ $L == >* ]]; then echo "$L"; else echo $L | rev | tr "ATGCatgc" "TACGtacg"; fi; done > output_file.txt
Hope it is useful for someone. It took me some time to build it.

Answer 4

The problem is that you're using -n in the perl flag, yet you've written your own loop. -n wraps your supplied code in a while loop like while(<STDIN>){...}. So the STDIN file handle has already been read from and your code does it again, getting EOF (end of file) or rather 'undefined'. You either need to remove the n from -ne or remove the while loop from your code.
Incidentally, a complete complement tr pattern, including ambiguous bases, is:
tr/ATGCBVDHRYKMatgcbvdhrykm/TACGVBHDYRMKtacgvbhdyrmk/
Ambiguous bases have complements too. For example, a V stands for an A, C, or G. Their complements are T, G, and C, which is represented by the ambiguous base B. Thus, V and B are complementary.
You don't need to include any N's or n's in your tr pattern (as was demonstrated in another answer) because the complement is the same and leaving them out will leave them untouched. It's just extra processing to put them in the pattern.