Question: Is there a way to get RNAFold output for multifasta in tabular format?
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adhirajnath14 • 40 wrote:
I am trying to calculate the MFE along with the secondary structure for multifasta using RNAFold. The output generated is of the format.
>abc GGCGGAGGUAGGGAGGCACGCGAUGGUAUUUCAGAGCCUCCCGAAUACAACUCCAGGGUAGGGUGUUGAAAGCGUUGGAGAUGUCUAAAGACACCGCCAG (((((.....(((((((.(..((.......)).).)))))))........((((((.((............)).)))))).((((....))))))))).. (-35.80) >lmn GGGAGGCACGCGAUGGUAUUUCAGAGCCUCCCGAAUACAACUCCAGGGUAGGGUGUUGAAAGCGUUGGAGAUGUCUAAAGACACCGCCAGUACCACCCCA (((((((.(..((.......)).).))))))).............((((..((((.........((((.(.((((....)))).).)))))))))))).. (-29.30) >xyz CGAUGGUAUUUCAGAGCCUCCCGAAUACAACUCCAGGGUAGGGUGUUGAAAGCGUUGGAGAUGUCUAAAGACACCGCCAGUACCACCCCACCCCGGGACA ....(((........)))(((((............((((.(((((.((......((((.(.((((....)))).).)))))).))))).))))))))).. (-28.40)
Is there a way to get the output in tubular format with 1. Identifier, 2. sequence, 3. secondary structure and 4. MFE as columns? I have written regular expression scripts to capture each of the four and paste it in a file but I don't think that's an efficient way of doing it. Is there any other convenient way of doing it?
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modified 16 months ago
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JC ♦ 12k
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16 months ago by
adhirajnath14 • 40
Regular expression capture groups is absolutely a valid way to do it, and probably the least hacky.
Otherwise, you would need to transliterate the
\n
characters to tabs, but since there are line wrappings, that will be much harder.