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RNAPARCONV(1) User Commands RNAPARCONV(1) NAME RNAparconv - manual page for RNAparconv 2.7.0 SYNOPSIS RNAparconv [options] [<input file>] [<output file>] DESCRIPTION RNAparconv 2.7.0 Convert energy parameter files from ViennaRNA 1.8.4 to 2.0 format Converts energy parameter files from "old" ViennaRNAPackage 1.8.4 for- mat to the new format used since ViennaRNAPackage 2.0. The Program reads a valid energy parameter file or valid energy parameters from stdin and prints the converted energy parameters to stdout or a speci- fied output file. Per default, the converted output file contains the whole set of energy parameters used throughout ViennaRNAPackage 1.8.4. The user can specify sets of energy parameters that should not be in- cluded in the output. -h, --help Print help and exit --detailed-help Print help, including all details and hidden options, and exit --full-help Print help, including hidden options, and exit -V, --version Print version and exit -v, --verbose Be verbose. (default=off) Lower the log level setting such that even INFO messages are passed through. I/O Options: Command line options for input and output (pre-)processing -i, --input=filename Specify an input file name. If argument is missing the energy parameter input can be supplied via 'stdin'. -o, --output=filename Specify an output file name. If argument is missing the con- verted energy parameters are printed to 'stdout'. --vanilla Print just as much as needed to represent the given energy para- meters data set. This option overrides all other output set- tings! (default=off) --dump Just dump Vienna 1.8.4 energy parameters in format used since 2.0. This option skips any energy parameter input! (default=off) --silent Print just energy parameters and appropriate comment lines but suppress all other output (default=off) --without-HairpinE Do not print converted hairpin energies and enthalpies (default=off) --without-StackE Do not print converted stacking energies and enthalpies (default=off) --without-IntE Do not print converted internal loop energies, enthalpies and asymetry factors (default=off) --without-BulgeE Do not print converted bulge loop energies and enthalpies (default=off) --without-MultiE Do not print converted multi loop energies and enthalpies (default=off) --without-MismatchE Do not print converted exterior loop mismatch energies and en- thalpies (default=off) --without-MismatchH Do not print converted hairpin mismatch energies and enthalpies (default=off) --without-MismatchI Do not print converted internal loop mismatch energies and en- thalpies (default=off) --without-MismatchM Do not print converted multi loop mismatch energies and en- thalpies (default=off) --without-Dangle5 Do not print converted 5' dangle energies and enthalpies (default=off) --without-Dangle3 Do not print converted 3' dangle energies and enthalpies (default=off) --without-Misc Do not print converted Misc energies and enthalpies (TerminalAU, DuplexInit, lxc) (default=off) --log-level=level Set log level threshold. (default=`2') By default, any log messages are filtered such that only warn- ings (level 2) or errors (level 3) are printed. This setting al- lows for specifying the log level threshold, where higher values result in fewer information. Log-level 5 turns off all messages, even errors and other critical information. --log-file[=filename] Print log messages to a file instead of stderr. (default=`RNA- parconv.log') --log-time Include time stamp in log messages. (default=off) --log-call Include file and line of log calling function. (default=off) REFERENCES If you use this program in your work you might want to cite: R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011), "ViennaRNA Package 2.0", Algorithms for Molecular Biology: 6:26 I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994), "Fast Folding and Comparison of RNA Secondary Struc- tures", Monatshefte f. Chemie: 125, pp 167-188 R. Lorenz, I.L. Hofacker, P.F. Stadler (2016), "RNA folding with hard and soft constraints", Algorithms for Molecular Biology 11:1 pp 1-13 The energy parameters are taken from: D.H. Mathews, M.D. Disney, D. Matthew, J.L. Childs, S.J. Schroeder, J. Susan, M. Zuker, D.H. Turner (2004), "Incorporating chemical modifica- tion constraints into a dynamic programming algorithm for prediction of RNA secondary structure", Proc. Natl. Acad. Sci. USA: 101, pp 7287-7292 D.H Turner, D.H. Mathews (2009), "NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure", Nucleic Acids Research: 38, pp 280-282 AUTHOR Ronny Lorenz REPORTING BUGS If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at. RNAparconv 2.7.0 October 2024 RNAPARCONV(1)
NAME | SYNOPSIS | DESCRIPTION | REFERENCES | AUTHOR | REPORTING BUGS
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