Command Line Tool To Obtain Complementary And/Or Inverse Strand From Fasta Files

Question

[etienne.decarie]

From a fasta file, I would like to obtain three new fasta files containing:

1. Inverse
2. Complement
3. Antiparallel

I am looking for a command line tool that can do what is provided on http://www.fr33.net/seqedit.php with fast files as input and output.

Python code to do the inverse, complement and antiparallel steps are available : http://zientzilaria.herokuapp.com/blog/2008/03/11/fasta-module-generating-reverse-complement-of-dna-sequences/

But I would like to integrate this so that it can be applied to fasta files (and not do the inverse, complement and antiparallel on the labels).

This is related to how to convert a big fasta file with multi-line DNA sequences into a fasta file of reverse complement sequence

[Whetting]

It looks like the answer to your question is in the links you provide?

[etienne.decarie]

The accepted answer is only for the reverse complement (ie antiparallel). I have tried getting biopieces to work on my system, but with no success.

[st.ph.n]

Your question title states you want a CLI tool. Then you mention Python. Which do you prefer? Biopieces would be the easiest way to go for CLI.

Answer 1

[Ido Tamir]

Your terminology is very confusing. The common names of these operations are reverse or complement which you can combine to the reverse complement.

In EMBOSS:

revseq test.fasta -reverse -complement -outseq test.revcomp.fasta
revseq test.fasta -noreverse -complement -outseq test.comp.fasta
revseq test.fasta -reverse -nocomplement -outseq test.rev.fasta

[etienne.decarie]

http://emboss.bioinformatics.nl/cgi-bin/emboss/help/revseq

[H.Hasani]

I don't think this program is doing the right thing, I'm getting the exact sequence with very minor differences and only the header of the sequences are changed to include Reversed

Answer 2

[Martin A Hansen]

Reversing and complementing sequences are separate tasks in Biopieces www.biopieces.org):

read_fasta -i in.fna | reverse_seq | write_fasta -o out.fna -x
read_fasta -i in.fna | complement_seq | write_fasta -o out.fna -x
read_fasta -i in.fna | reverse_seq | complement_seq | write_fasta -o out.fna -x

Answer 3

[melendezmatias]

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 &gt;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

[JC]

Perl solution:

#!/usr/bin/perl

use strict;
use warnings;

$ARGV[0] or die "usage: convertFasta.pl FILE\n";
my $file = shift @ARGV;
$/ = "\n>"; 
open F, "$file" or die;
open A, ">$file.antiparallel" or die;
open I, ">$file.inverse" or die;
open C, ">$file.complement" or die;

while (<F>) {
    my ($id, @seq) = split (/\n/, $_);
    my $seq = join "", @seq;
    my $seq_complement = $seq; 
    $seq_complement =~ tr/ACGTacgt/TGCAtgca/;
    my $seq_inverse = reverse $seq;
    my $seq_antiparallel = $seq_inverse;
    $seq_antiparallel =~ tr/ACGTacgt/TGCAtgca/;

    print I "$id\n$seq_inverse";
    print C "$id\n$seq_complement";
    print A "$id\n$seq_antiparallel";
}