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=27834view=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=27834r1=27833r2=27834view=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,
