URL:
<http://gna.org/bugs/?7697>
Summary: Ambiguous errors for hybrid models
Project: relax
Submitted by: viochemist
Submitted on: Friday 11/10/2006 at 08:56
Category: relax's source code
Priority: 5 - Normal
Severity: 2 - Minor
Status: None
Privacy: Public
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Release: Repository: 1.3 line
Operating System: All systems
_______________________________________________________
Details:
Copied from Message-id:
<481156b20611091000u4e57019if293aa311044e99d@xxxxxxxxxxxxxx>
I'm trying to run a hybrid model selection on my data and have been getting a
Traceback error. This is my script and the output.
script = 'my_hybrid.py'
----------------------------------------------------------------------------------------------------
run.create('Dom1','mf')
run.create('Dom2','mf')
run.create('hybrid_select','mf')
results.read('Dom1','results.bz2','15N_final_domain1/final')
results.read('Dom2','results.bz2','15N_final_domain2/final')
run.hybridise('hybrid',['Dom1','Dom2'])
model_selection('AIC','hybrid_select',['Dom1','Dom2','hybrid'])
----------------------------------------------------------------------------------------------------
relax> run.create(run='Dom1', run_type='mf')
relax> run.create(run='Dom2', run_type='mf')
relax> run.create(run='hybrid_select', run_type='mf')
relax> results.read(run='Dom1', file='results.bz2',
dir='15N_final_domain1/final', format='columnar')
Opening the file '15N_final_domain1/final/results.bz2' for reading.
Loading all structures from the PDB file.
Structure('etar_au22_phage_df_pt.pdb', model=1):
Nucleotide chain of length 68
relax> results.read(run='Dom2', file='results.bz2',
dir='15N_final_domain2/final', format='columnar')
Opening the file '15N_final_domain2/final/results.bz2' for reading.
Using the structures from the run 'Dom1'.
Structure('etar_au22_phage_df_pt.pdb', model=1):
Nucleotide chain of length 68
relax> run.hybridise(hybrid='hybrid', runs=['Dom1', 'Dom2'])
relax> model_selection(method='AIC', modsel_run='hybrid_select',
runs=['Dom1', 'Dom2', 'hybrid'])
AIC model selection.
Instance 0.
Run Num_params_(k) Num_data_sets_(n) Chi2
Criterion
Dom1 9 12 3.70303
21.70303
Dom2 10 12 1.89550
21.89550
Traceback (most recent call last):
File "relax", line 454, in ?
Relax()
File "relax", line 166, in __init__
self.interpreter.run()
File "/local/home/viochem/relax/prompt/interpreter.py", line 213, in run
run_script(intro=self.relax.intro_string, local= self.local,
script_file=self.relax.script_file, quit=1)
File "/local/home/viochem/relax/prompt/interpreter.py", line 388, in
run_script
console.interact(intro, local, script_file, quit)
File "/local/home/viochem/relax/prompt/interpreter.py", line 340, in
interact_script
execfile(script_file, local)
File "my_hybrid.py", line 9, in ?
model_selection('AIC','hybrid_select',['Dom1','Dom2','hybrid'])
File "/local/home/viochem/relax/prompt/model_selection.py", line 121, in
model_selection
self.relax.generic.model_selection.select(method=method,
modsel_run=modsel_run, runs=runs)
File "/local/home/viochem/relax/generic_fns/model_selection.py", line 217,
in select
k, n, chi2 = self.model_statistics [run](run=run, instance=i,
global_stats=global_stats)
File "/local/home/viochem/relax/specific_fns/hybrid.py", line 117, in
model_statistics
for i in xrange(num):
NameError: global name 'num' is not defined
Is this a bug, or am I doing something totally wrong?
_______________________________________________________
Follow-up Comments:
-------------------------------------------------------
Date: Friday 11/10/2006 at 08:56 By: Alex Hansen <Alex Hansen>
Copied from Message-id:
<481156b20611091000u4e57019if293aa311044e99d@xxxxxxxxxxxxxx>
I'm trying to run a hybrid model selection on my data and have been getting a
Traceback error. This is my script and the output.
script = 'my_hybrid.py'
----------------------------------------------------------------------------------------------------
run.create('Dom1','mf')
run.create('Dom2','mf')
run.create('hybrid_select','mf')
results.read('Dom1','results.bz2','15N_final_domain1/final')
results.read('Dom2','results.bz2','15N_final_domain2/final')
run.hybridise('hybrid',['Dom1','Dom2'])
model_selection('AIC','hybrid_select',['Dom1','Dom2','hybrid'])
----------------------------------------------------------------------------------------------------
relax> run.create(run='Dom1', run_type='mf')
relax> run.create(run='Dom2', run_type='mf')
relax> run.create(run='hybrid_select', run_type='mf')
relax> results.read(run='Dom1', file='results.bz2',
dir='15N_final_domain1/final', format='columnar')
Opening the file '15N_final_domain1/final/results.bz2' for reading.
Loading all structures from the PDB file.
Structure('etar_au22_phage_df_pt.pdb', model=1):
Nucleotide chain of length 68
relax> results.read(run='Dom2', file='results.bz2',
dir='15N_final_domain2/final', format='columnar')
Opening the file '15N_final_domain2/final/results.bz2' for reading.
Using the structures from the run 'Dom1'.
Structure('etar_au22_phage_df_pt.pdb', model=1):
Nucleotide chain of length 68
relax> run.hybridise(hybrid='hybrid', runs=['Dom1', 'Dom2'])
relax> model_selection(method='AIC', modsel_run='hybrid_select',
runs=['Dom1', 'Dom2', 'hybrid'])
AIC model selection.
Instance 0.
Run Num_params_(k) Num_data_sets_(n) Chi2
Criterion
Dom1 9 12 3.70303
21.70303
Dom2 10 12 1.89550
21.89550
Traceback (most recent call last):
File "relax", line 454, in ?
Relax()
File "relax", line 166, in __init__
self.interpreter.run()
File "/local/home/viochem/relax/prompt/interpreter.py", line 213, in run
run_script(intro=self.relax.intro_string, local= self.local,
script_file=self.relax.script_file, quit=1)
File "/local/home/viochem/relax/prompt/interpreter.py", line 388, in
run_script
console.interact(intro, local, script_file, quit)
File "/local/home/viochem/relax/prompt/interpreter.py", line 340, in
interact_script
execfile(script_file, local)
File "my_hybrid.py", line 9, in ?
model_selection('AIC','hybrid_select',['Dom1','Dom2','hybrid'])
File "/local/home/viochem/relax/prompt/model_selection.py", line 121, in
model_selection
self.relax.generic.model_selection.select(method=method,
modsel_run=modsel_run, runs=runs)
File "/local/home/viochem/relax/generic_fns/model_selection.py", line 217,
in select
k, n, chi2 = self.model_statistics [run](run=run, instance=i,
global_stats=global_stats)
File "/local/home/viochem/relax/specific_fns/hybrid.py", line 117, in
model_statistics
for i in xrange(num):
NameError: global name 'num' is not defined
Is this a bug, or am I doing something totally wrong?
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[bug #7697] Ambiguous errors for hybrid models