RNAparconv#
RNAparconv - manual page for RNAparconv 2.7.2
Synopsis#
RNAparconv [options] [<input file>] [<output file>]
DESCRIPTION#
RNAparconv 2.7.2
Convert energy parameter files from ViennaRNA 1.8.4 to 2.0 format
Converts energy parameter files from “old” ViennaRNAPackage 1.8.4 format 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 specified 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 included in the output.
- -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 converted energy parameters are printed to
stdout.
- --vanilla#
Print just as much as needed to represent the given energy parameters data set. This option overrides all other output settings!
(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 enthalpies
(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 enthalpies
(default=off)
- --without-MismatchM#
Do not print converted multi loop mismatch energies and enthalpies
(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 warnings (level 2) or errors (level 3) are printed. This setting allows 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=”RNAparconv.log”)
- --log-time#
Include time stamp in log messages.
(default=off)
- --log-call#
Include file and line of log calling function.
(default=off)
- -h, --help#
display help and exit
- --full-help#
display help, including hidden options, and exit
- --detailed-help#
display help, including all details and hidden options, and exit
- -V, --version#
output version and exit
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 Structures”, 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 modification 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
REPORTING BUGS#
If in doubt our program is right, nature is at fault. Comments should be sent to rna@tbi.univie.ac.at.