Hi Troels, Another point for the new write_convert_file() method, would this be doable as a Python rather than Bash script? This addition makes the analysis GNU/Linux or Mac OS X specific, and MS Windows users miss out. Or am I missing something?
Cheers, Edward On 27 May 2015 at 03:09, <tlin...@nmr-relax.com> wrote: > Author: tlinnet > Date: Wed May 27 03:09:35 2015 > New Revision: 27834 > > URL: http://svn.gna.org/viewcvs/relax?rev=27834&view=rev > Log: > Wrote a method to store parameter data and dispersion curves, for the > protocol of repeated analysis. > > This is to prepare for analysis in other programs. > The method loops throug the data pipes, and write the data out. > > It then write a bash script, that will concatenate the data in an matrix > array style, for reading and processing in other programs. > > Task #7826 (https://gna.org/task/?7826): Write an python class for the > repeated analysis of dispersion data. > > Modified: > trunk/auto_analyses/relax_disp_repeat_cpmg.py > > Modified: trunk/auto_analyses/relax_disp_repeat_cpmg.py > URL: > http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/relax_disp_repeat_cpmg.py?rev=27834&r1=27833&r2=27834&view=diff > ============================================================================== > --- trunk/auto_analyses/relax_disp_repeat_cpmg.py (original) > +++ trunk/auto_analyses/relax_disp_repeat_cpmg.py Wed May 27 03:09:35 > 2015 > @@ -32,10 +32,11 @@ > from copy import deepcopy > from datetime import datetime > from glob import glob > -from os import F_OK, access, getcwd, sep > +from os import F_OK, access, chmod, getcwd, sep > from numpy import any, asarray, arange, concatenate, max, mean, min, sqrt, > std, sum > if dep_check.scipy_module: > from scipy.stats import pearsonr > +from stat import S_IRWXU, S_IRGRP, S_IROTH > import sys > from warnings import warn > > @@ -48,7 +49,7 @@ > from pipe_control.mol_res_spin import display_spin, generate_spin_string, > return_spin, spin_loop > from pipe_control import pipes > from prompt.interpreter import Interpreter > -from specific_analyses.relax_disp.data import generate_r20_key, > has_exponential_exp_type, is_r1_optimised, loop_exp_frq_offset, > loop_exp_frq_offset_point, return_param_key_from_data > +from specific_analyses.relax_disp.data import generate_r20_key, > has_exponential_exp_type, has_cpmg_exp_type, is_r1_optimised, > loop_exp_frq_offset, loop_exp_frq_offset_point, return_param_key_from_data > from status import Status; status = Status() > > if dep_check.matplotlib_module: > @@ -2665,6 +2666,149 @@ > plt.show() > > > + def write_results(self, method=None, model=None, analysis=None, > list_glob_ini=None, selection=None): > + > + for glob_ini in list_glob_ini: > + # Check previous, and get the pipe name. > + found, pipe_name, resfile, path = > self.check_previous_result(method=method, model=model, analysis=analysis, > glob_ini=glob_ini, bundle=method) > + > + if pipes.cdp_name() != pipe_name: > + self.interpreter.pipe.switch(pipe_name) > + > + # Printout. > + section(file=sys.stdout, text="Results writing for > pipe='%s"%(pipe_name), prespace=2, postspace=0) > + model_params = MODEL_PARAMS[model] > + subsection(file=sys.stdout, text="Model %s, with > params='%s"%(model, model_params), prespace=0) > + > + # Set path > + model_path = model.replace(" ", "_") > + analysis_path = analysis.replace(" ", "_") > + path = self.results_dir+sep+model_path+sep+analysis_path > + > + # Dispersion curves. > + path_disp = path+sep+"disp_curves"+sep+method+sep+str(glob_ini) > + self.interpreter.relax_disp.plot_disp_curves(dir=path_disp, > force=True) > + self.interpreter.relax_disp.write_disp_curves(dir=path_disp, > force=True) > + > + # The selected models for the final run. > + self.interpreter.value.write(param='model', file='model.out', > dir=path, force=True) > + > + models_tested = None > + > + # For CPMG models. > + filep = str(glob_ini)+"_"+method+"_" > + path_par = path+sep+"r2" > + if has_cpmg_exp_type(): > + # The R20 parameter. > + self.write_results_test(path=path_par, model=model, > models_tested=models_tested, param='r2', file_name_ini=filep+'r20') > + > + # The R20A and R20B parameters. > + self.write_results_test(path=path_par, model=model, > models_tested=models_tested, param='r2a', file_name_ini=filep+'r20a') > + self.write_results_test(path=path_par, model=model, > models_tested=models_tested, param='r2b', file_name_ini=filep+'r20b') > + > + # The pA and pB parameters. > + path_par = path+sep+"pop" > + self.write_results_test(path=path_par, model=model, > models_tested=models_tested, param='pA', file_name_ini=filep+'pA') > + self.write_results_test(path=path_par, model=model, > models_tested=models_tested, param='pB', file_name_ini=filep+'pB') > + > + # The dw parameter. > + path_par = path+sep+"dw" > + search = method+"_"+"dw" > + self.write_results_test(path=path_par, model=model, > models_tested=models_tested, search=search, param='dw', > file_name_ini=filep+'dw') > + > + # The k_AB, kex and tex parameters. > + path_par = path+sep+"rate" > + self.write_results_test(path=path_par, model=model, > models_tested=models_tested, param='k_AB', file_name_ini=filep+'k_AB') > + self.write_results_test(path=path_par, model=model, > models_tested=models_tested, param='kex', file_name_ini=filep+'kex') > + self.write_results_test(path=path_par, model=model, > models_tested=models_tested, param='tex', file_name_ini=filep+'tex') > + > + # Minimisation statistics. > + if not (model == MODEL_R2EFF and has_fixed_time_exp_type()): > + path_par = path+sep+"chi2" > + self.interpreter.value.write(param='chi2', > file=filep+'chi2.out', dir=path_par, force=True) > + self.interpreter.grace.write(y_data_type='chi2', > file='chi2.agr', dir=path_par+sep+"grace", force=True) > + > + > + def write_results_test(self, path=None, model=None, models_tested=None, > search=None, param=None, file_name_ini=None): > + """Create a set of results, text and Grace files for the current > data pipe. > + > + @keyword path: The directory to place the files into. > + @type path: str > + @keyword model: The model tested. > + @type model: None or str > + @keyword model_tested: List of models tested, if the pipe is > final. > + @type model_tested: None or list of str. > + @keyword param: The param to write out. > + @type param: None or list of str. > + @keyword file_name_ini: The initial part of the file name for > the grace and text files. > + @type file_name_ini: None or str. > + """ > + > + # If not set, use the name of the parameter. > + if file_name_ini == None: > + file_name_ini = param > + > + # If the model is in the list of models which support the parameter. > + write_result = False > + if model != None: > + # Get the model params. > + model_params = MODEL_PARAMS[model] > + > + if param in model_params: > + write_result = True > + > + # If this is the final pipe, then check if the model has been tested > at any time. > + elif model == None: > + # Loop through all tested models. > + for model_tested in models_tested: > + # If one of the models tested has a parameter which belong > in the list of models which support the parameter, then write it out. > + model_params = MODEL_PARAMS[model_tested] > + > + if param in model_params: > + write_result = True > + break > + > + # Write results if some of the models supports the parameter. > + if write_result: > + self.interpreter.value.write(param=param, > file='%s.out'%file_name_ini, dir=path, force=True) > + # Write convert file > + if search != None: > + col_file_name="collect_%s.sh"%search > + self.write_convert_file(file_name=col_file_name, path=path, > search=search) > + > + # Write grace > + self.interpreter.grace.write(x_data_type='res_num', > y_data_type=param, file='%s.agr'%file_name_ini, dir=path+sep+"grace", > force=True) > + > + > + def write_convert_file(self, file_name=None, path=None, search=None): > + file_obj, file_path = open_write_file(file_name=file_name, dir=path, > force=True, compress_type=0, verbosity=1, return_path=True) > + > + # Write file > + file_obj.write('#! /bin/bash' + '\n') > + file_obj.write('SEARCH=%s'%(search) + '\n') > + file_obj.write('FILES=(*_${SEARCH}.out)' + '\n') > + file_obj.write('readarray -t FILESSORT < <(for a in "${FILES[@]}"; > do echo "$a"; done | sort -Vr)' + '\n') > + file_obj.write('# Skip the first two lines of header' + '\n') > + file_obj.write("tail -n+3 ${FILESSORT[0]} | sed 's,^# ,,' | awk > '{print $2,$3,$5}' | column -t > collect_${SEARCH}.tmp" + '\n') > + file_obj.write('# Make array' + '\n') > + file_obj.write('ACUT=(collect_${SEARCH}.tmp)' + '\n') > + file_obj.write('for f in "${FILESSORT[@]}"; do' + '\n') > + file_obj.write(' FNAME="${f%.*}"' + '\n') > + file_obj.write(' NI=`echo $f | cut -d"_" -f1`' + '\n') > + file_obj.write(' echo "Processing $f with NI=$NI"' + '\n') > + file_obj.write(' tail -n+3 $f | sed "s,^# ,," | sed > "s,value,${NI}," | sed "s,error,${NI}," | awk %s{print $6,$7}%s | column -t > > ${FNAME}.tmp'%("'","'") + '\n') > + file_obj.write(' ACUT+=(${FNAME}.tmp)' + '\n') > + file_obj.write('done' + '\n') > + file_obj.write('paste "${ACUT[@]}" | column -t > > collect_${SEARCH}.txt' + '\n') > + file_obj.write('rm ${ACUT[@]}' + '\n') > + > + > + # Close the batch script, then make it executable (expanding any ~ > characters). > + file_obj.close() > + > + chmod(file_path, S_IRWXU|S_IRGRP|S_IROTH) > + > + > def interpreter_start(self): > # Load the interpreter. > self.interpreter = Interpreter(show_script=False, > raise_relax_error=True) > > > _______________________________________________ > relax (http://www.nmr-relax.com) > > This is the relax-commits mailing list > relax-comm...@gna.org > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-commits _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel
