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)
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Re: r27834 - /trunk/auto_analyses/relax_disp_repeat_cpmg.py