URL:
<http://gna.org/bugs/?20873>
Summary: Custom Peak intensity reading cannot read a list of
spectrum_id
Project: relax
Submitted by: tlinnet
Submitted on: Thu 06 Jun 2013 02:58:58 PM GMT
Category: relax's source code
Severity: 3 - Normal
Priority: 5 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Name:
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Release: Repository: trunk
Operating System: GNU/Linux
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Details:
See: http://article.gmane.org/gmane.science.nmr.relax.user/1452
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Using a Generic intensity file.
The input of the spectrum id is converted to a string, and not a list or
tuble.
spectrum_id='(2,6)'
is translated to a string.
This should be corrected, to do similar as the intensity columns:
int_col=(6, 7)
----------------------------------
To reproduce error
----------------------------------
Start new analysis
Relaxation dispersion analysis
Relaxation dispersion experiment type selection
CPMG, fixed time
Data pipe set up
The starting data pipe for the analysis = origin - relax_disp
The data pipe bundle = relax_disp
Spin editor
Click: Spin editor
Click: Load spins
Click: From a file containing sequence data
The file name = test.seq
The spin ID string = Leave empty
Free format
Molecule name column (mol_name_col) = 1
Residue number column (res_num_col) = 2
Residue name column (res_name_col) = 3
Spin number column (spin_num_col) = 4
Spin name column (spin_name_col) = 5
Add spectra
Click "Add"
The file name = test.seq
The Spectrum ID string: 2,0
The Intensity column: 6,7
rest is default
Error:
No corresponding data could be found within the file.
ERROR:
relax> spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/test.seq',
dir=None, spectrum_id='2,0', heteronuc='N', proton='HN', int_method='height',
int_col=(6, 7), spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None,
ncproc=None)
Opening the file '/sbinlab2/tlinnet/Desktop/test.seq' for reading.
Generic formatted data file.
.....
RelaxWarning: The sequence data in the line ['protein', '75', 'L', '75', 'N',
'3.578841e+06', '6.352595e+06'] is invalid, the data is missing.
RelaxError: No corresponding data could be found within the file.
In prompt:
pipe.create(pipe_name='origin rx', pipe_type='relax_disp', bundle='rx')
relax_disp.exp_type(exp_type='cpmg fixed')
sequence.read(file='/sbinlab2/tlinnet/Desktop/test.seq',
dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None,
spin_id=None)
spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/test.seq',
dir=None, spectrum_id=(2,0), heteronuc='N', proton='HN',
int_method='height', int_col=(6, 7), spin_id_col=None, mol_name_col=1,
res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5,
sep=None, spin_id=None, ncproc=None)
File "<input>", line 3, in <module>
File "/sbinlab2/software/NMR-relax/relax_disp/prompt/uf_objects.py",
line 200, in __call__
lib.arg_check.is_str(value, desc_short, can_be_none=can_be_none)
File "/sbinlab2/software/NMR-relax/relax_disp/lib/arg_check.py",
line 862, in is_str
raise RelaxStrError(name, arg)
RelaxStrError: [31mRelaxError: The spectrum ID string argument '(2,0)' must
be a string. [0m
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Thu 06 Jun 2013 02:58:58 PM GMT Name: test.seq Size: 432B By:
tlinnet
<http://gna.org/bugs/download.php?file_id=18054>
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[bug #20873] Custom Peak intensity reading cannot read a list of spectrum_id