URL:
<http://gna.org/bugs/?17213>
Summary: Setting of parameter file columns fails if a column
is missing.
Project: relax
Submitted by: bugman
Submitted on: Fri 03 Dec 2010 04:38:21 PM GMT
Category: GUI
Severity: 5 - Blocker
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: michaelbieri
Originator Name:
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Release: Branches
Operating System: All systems
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Details:
If the relaxation data file for model-free analysis is missing a column (e.g.
molecule name, spin number, etc.) then an error is thrown. The problem is in
the conversion of empty strings '' to ints, instead of None. The traceback
is:
Starting model-free calculation
-------------------------------
relax> pipe.create(pipe_name='tm0', pipe_type='mf')
relax>
sequence.read(file='/media/disk/relax/sebastian/for_Edward/PSE-4/step_1__full_analysis__sec_struc/consistent_Ambler_500_R2_plus_sequence_erreur_min_mean',
dir=None, spin_id_col=None, mol_name_col=None, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, sep=None, spin_id=None)
/media/disk/relax/sebastian/for_Edward/PSE-4/step_1__full_analysis__sec_struc/consistent_Ambler_500_R2_plus_sequence_erreur_min_mean
None
Opening the file
'/media/disk/relax/sebastian/for_Edward/PSE-4/step_1__full_analysis__sec_struc/consistent_Ambler_500_R2_plus_sequence_erreur_min_mean'
for reading.
Unhandled exception in thread started by
Traceback (most recent call last):
File
"/media/disk/relax/branches/bieri_gui/gui_bieri/analyses/auto_model_free.py",
line 856, in execute_thread
dAuvergne_protocol(save_dir=data.save_dir, diff_model=global_model,
mf_models=data.mf_models, local_tm_models=data.local_tm_models,
pdb_file=data.structure_file, seq_args=data.seq_args, het_name=data.het_name,
relax_data=data.relax_data, unres=data.unres, exclude=data.exclude,
bond_length=data.bond_length, csa=data.csa, hetnuc=data.hetnuc,
proton=data.proton, grid_inc=data.inc, min_algor=data.min_algor,
mc_num=data.mc_num, max_iter=data.max_iter, conv_loop=data.conv_loop)
File
"/media/disk/relax/branches/bieri_gui/auto_analyses/dauvergne_protocol.py",
line 277, in __init__
self.multi_model(local_tm=True)
File
"/media/disk/relax/branches/bieri_gui/auto_analyses/dauvergne_protocol.py",
line 815, in multi_model
self.interpreter.sequence.read(file=self.seq_args[0],
dir=self.seq_args[1], mol_name_col=self.seq_args[2],
res_num_col=self.seq_args[3], res_name_col=self.seq_args[4],
spin_num_col=self.seq_args[5], spin_name_col=self.seq_args[6],
sep=self.seq_args[7])
File "/media/disk/relax/branches/bieri_gui/prompt/sequence.py", line 244,
in read
sequence.read(file=file, dir=dir, spin_id_col=spin_id_col,
mol_name_col=mol_name_col, res_num_col=res_num_col, res_name_col=res_name_col,
spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep,
spin_id=spin_id)
File "/media/disk/relax/branches/bieri_gui/generic_fns/sequence.py", line
293, in read
for id in read_spin_data(file=file, dir=dir, file_data=file_data,
spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, sep=sep, spin_id=spin_id):
File "/media/disk/relax/branches/bieri_gui/relax_io.py", line 601, in
read_spin_data
raise RelaxError("No corresponding data could be found within the
file.")
relax_errors.RelaxError: RelaxError: No corresponding data could be found
within the file.
Unhandled exception in thread started by
Traceback (most recent call last):
File
"/media/disk/relax/branches/bieri_gui/gui_bieri/analyses/auto_model_free.py",
line 838, in execute_thread
data = self.assemble_data()
File
"/media/disk/relax/branches/bieri_gui/gui_bieri/analyses/auto_model_free.py",
line 565, in assemble_data
data.seq_args = [sequence_file, None, None, int(param[1]),
int(param[2]),int(param[3]), int(param[4]), None]
ValueError: invalid literal for int() with base 10: ''
_______________________________________________________
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[bug #17213] Setting of parameter file columns fails if a column is missing.