Is there a way to get RNAFold output for multifasta in tabular format?

>abc GGCGGAGGUAGGGAGGCACGCGAUGGUAUUUCAGAGCCUCCCGAAUACAACUCCAGGGUAGGGUGUUGAAAGCGUUGGAGAUGUCUAAAGACACCGCCAG (((((.....(((((((.(..((.......)).).)))))))........((((((.((............)).)))))).((((....))))))))).. (-35.80) >lmn GGGAGGCACGCGAUGGUAUUUCAGAGCCUCCCGAAUACAACUCCAGGGUAGGGUGUUGAAAGCGUUGGAGAUGUCUAAAGACACCGCCAGUACCACCCCA (((((((.(..((.......)).).))))))).............((((..((((.........((((.(.((((....)))).).)))))))))))).. (-29.30) >xyz CGAUGGUAUUUCAGAGCCUCCCGAAUACAACUCCAGGGUAGGGUGUUGAAAGCGUUGGAGAUGUCUAAAGACACCGCCAGUACCACCCCACCCCGGGACA ....(((........)))(((((............((((.(((((.((......((((.(.((((....)))).).)))))).))))).))))))))).. (-28.40)

16 months ago by

JC ♦ 12k

Mexico

JC ♦ 12k wrote:

In Perl:

#!/usr/bin/perl

use strict;
use warnings;

while (<>) {
    chomp;
    if (/>/) {
        s/>//;
        print "$_\t"; # just the seq id
    }
    elsif (/\((-\d+\.\d+)\)$/) {
        my $mfe = $1;
        s/ \($mfe\)//;
        print "$_\t$mfe\n"; # fold + MFE
    }
    else {
        print "$_\t"; # the seq
    }
}

Validation:

$ perl fold2tab.pl < fold.fa
abc     GGCGGAGGUAGGGAGGCACGCGAUGGUAUUUCAGAGCCUCCCGAAUACAACUCCAGGGUAGGGUGUUGAAAGCGUUGGAGAUGUCUAAAGACACCGCCAG    (((((.....(((((((.(..((.......)).).)))))))........((((((.((............)).)))))).((((....)))))))))..     -35.80
lmn     GGGAGGCACGCGAUGGUAUUUCAGAGCCUCCCGAAUACAACUCCAGGGUAGGGUGUUGAAAGCGUUGGAGAUGUCUAAAGACACCGCCAGUACCACCCCA    (((((((.(..((.......)).).))))))).............((((..((((.........((((.(.((((....)))).).))))))))))))..     -29.30
xyz     CGAUGGUAUUUCAGAGCCUCCCGAAUACAACUCCAGGGUAGGGUGUUGAAAGCGUUGGAGAUGUCUAAAGACACCGCCAGUACCACCCCACCCCGGGACA    ....(((........)))(((((............((((.(((((.((......((((.(.((((....)))).).)))))).))))).)))))))))..     -28.40

ADD COMMENT • link modified 16 months ago • written 16 months ago by JC ♦ 12k

One-liner:

$ perl -pe 's/\n/\t/g; s/>//; s/\s+/\t/; s/\(-/-/; s/\)\t$/\n/' < fold.fa
abc     GGCGGAGGUAGGGAGGCACGCGAUGGUAUUUCAGAGCCUCCCGAAUACAACUCCAGGGUAGGGUGUUGAAAGCGUUGGAGAUGUCUAAAGACACCGCCAG    (((((.....(((((((.(..((.......)).).)))))))........((((((.((............)).)))))).((((....)))))))))..    -35.80
lmn     GGGAGGCACGCGAUGGUAUUUCAGAGCCUCCCGAAUACAACUCCAGGGUAGGGUGUUGAAAGCGUUGGAGAUGUCUAAAGACACCGCCAGUACCACCCCA    (((((((.(..((.......)).).))))))).............((((..((((.........((((.(.((((....)))).).))))))))))))..    -29.30
xyz     CGAUGGUAUUUCAGAGCCUCCCGAAUACAACUCCAGGGUAGGGUGUUGAAAGCGUUGGAGAUGUCUAAAGACACCGCCAGUACCACCCCACCCCGGGACA    ....(((........)))(((((............((((.(((((.((......((((.(.((((....)))).).)))))).))))).)))))))))..    -28.40

ADD REPLY • link written 16 months ago by JC ♦ 12k

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