Command-line options

RASP Command-line Options

RASP accepts the following command-line options.
Other options or arguments will raise an error.

General Options |
--------------------------------|---
-h, --help |Show a brief help message and exit.
-v, --verbose |Write very detailed output to the log file for debugging. Because this can result in very large log files, it is advisable to use only 0 or 1 RASP iterations in this mode.
--version |Show the RASP version and exit.

File IO options: |
--------------------------------|---
-n name, --name=name |Set the base name for all input and output files. Input will be read from name_expt.tab and name_pred.tab, and output written to name_ss.out and name_res.out. The RASP log will be written to name.log. By default, name = rasp. Individual file names can be overriden with the options –p, -e, -l, and –o, as described below.
-p file, --predicted= file |Set the filename to read predicted chemical shifts from. By default this is set according to the base name set with –n above.
-e file, --spinSystems=file |Set the filename to read predicted chemical shifts from. By default this is set according to the base name set with –n above.
-l logfile, --log=logfile |Set the filename for saving the RASP log. By default this is set according to the base name set with –n above.
-o outname, --output=outname |Set the base name for result output. The assignment ensemble that results from a RASP run is output as two files, outname_ss.out and outname_res.out. By default outname=name.
-c project, --analysis=project|Read experimental shifts from CCPNMR Analysis project. This requires that RASP be run with the same Python version that Analysis is running. The analysis project must be setup with the desired spin systems defined, with intra-residue and inter-residue resonances properly defined. This feature is currently experimental, and not well tested: please check carefully that it is doing what you want.
-w, --write_state |Write final program state to file. RASP state files allow interactive analysis of the program state at the end of a run. They are useful for advanced/customised analysis of the assignment ensemble and underlying data. They can also be useful for debugging. They are not intended as containers for long-term data storage: in particular, no guarantee is offered that RASP state files will be readable by subsequent versions of the software or even the same version of the software running on a different platform. The default is not to write a state file. If –w is given, by default the state file will be written to outname.state, though this can be overridden by passing –stateFile.
--stateFile=stateFile |Set the file name to write program state to. By default stateFile=name or, if –o is given, stateFile=outname. Implies –w.

Algorithm control options: |
--------------------------------|---
-2, --two |Conduct the GRASP construction phase pair-wise, rather than by triplet. This approach is less demanding of memory, so may be useful for very large proteins. Any advantage in construction times, however, are likely to be undermined by longer local search phase. The resulting assignment ensemble is typically more diverse, so coverage is reduced relative to the standard triplet construction.
-s func, --similarity=func |Use func as the similarity function, the first term in the RASP scoring function. func can take the values dist, nds or sim, where dist is the simple shift distance between spin system and residue, nds is the normalised distance, and sim the default RASP similarity score. In the nomenclature used below, dist = D, nds = N and sim = L. By default, func=sim.
-f file, --fix=file |Fix the assignment of a subset of spin systems. Assignments to be fixed are read from file: one assignment is read per line, with the first term the spin system ID, the second term the residue ID to which the spin system is to be assigned. All other terms are assumed to be comments and are ignored.
-i nIter, --iterations=nIter |Run nIter RASP iterations, to yield an assignment ensemble of nIter members. By default nIter=100.
--nproc=nProc |If nProc > 1, run RASP iterations over nProc processes in parallel. This uses the Python multiprocessing framework. For optimal performance with nIter ≥ 50, choose nProc=6-8, but less than the number of available processors.

Options useful for testing |
--------------------------------|---
-t, --testmode |Assemble spin systems from chemical shifts read from an assigned dataset. Assigned chemical shifts will be read from the file specified by –e in any of the formats RASP reads predicted shifts from.
-a atoms, --atoms=atoms |Consider only atoms when calculating the RASP scoring function. atoms is a comma-separated list of atom names, appended by - for i-1 atoms. So atoms=h,n,c-,ca,ca- limits the analysis to HNCO/HNCA spin systems. By default, RASP considers all available atoms.