Hi,
There are a number of problems - my automatic parsing is pulling out a
lot of mess :S Unfortunately every second file appears to be
triggering a failure (maybe half of these are bugs in bmrblib
(http://gna.org/projects/bmrblib/)). For example the file
bmr15097.str in the v3.1 format is so corrupted pystarlib cannot even
handle it:
-----------------------------------
bmr3.1_files/bmr15097.str
relax> pipe.create(pipe_name='bmr15097.str', pipe_type='mf')
relax> bmrb.read(file='bmr3.1_files/bmr15097.str', dir=None,
version='3.1')
ERROR in semicolon_block_collapse for text starting at: [; 15097 1
stop_
loop_
_Task.Task
_Task.Entry_ID
_Task.Software_ID
]
Traceback (most recent call last):
File "/media/disk/relax/branches/bmrb/relax", line 381, in<module>
Relax()
File "/media/disk/relax/branches/bmrb/relax", line 117, in __init__
self.interpreter.run(self.script_file)
File "/media/disk/relax/branches/bmrb/prompt/interpreter.py", line 294,
in run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
File "/media/disk/relax/branches/bmrb/prompt/interpreter.py", line
597, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/media/disk/relax/branches/bmrb/prompt/interpreter.py", line
483, in interact_script
exec_script(script_file, local)
File "/media/disk/relax/branches/bmrb/prompt/interpreter.py", line
376, in exec_script
runpy.run_module(module, globals)
File "/usr/lib64/python2.6/runpy.py", line 140, in run_module
fname, loader, pkg_name)
File "/usr/lib64/python2.6/runpy.py", line 34, in _run_code
exec code in run_globals
File "/data/edau/bmrb/data_mining/read.py", line 44, in<module>
bmrb.read(path, version=version)
File "/media/disk/relax/branches/bmrb/prompt/bmrb.py", line 209, in read
bmrb.read(file=file, directory=dir, version=version)
File "/media/disk/relax/branches/bmrb/generic_fns/bmrb.py", line 144, in
read
read_function(file_path, version=version)
File "/media/disk/relax/branches/bmrb/specific_fns/model_free/bmrb.py",
line 295, in bmrb_read
star.read()
File "/media/disk/relax/branches/bmrb/bmrblib/nmr_star_dict.py",
line 98, in read
self.data.read()
File "/media/disk/relax/branches/bmrb/bmrblib/pystarlib/File.py",
line 89, in read
if self.parse(text=text, nmrView_type = nmrView_type):
File "/media/disk/relax/branches/bmrb/bmrblib/pystarlib/File.py",
line 117, in parse
text = semicolon_block_collapse(text)
File "/media/disk/relax/branches/bmrb/bmrblib/pystarlib/Text.py",
line 361, in semicolon_block_collapse
endpos = startpos + 1 + semicolon_end.end() -
len(semicolon_end.group(1)) + 1
AttributeError: 'NoneType' object has no attribute 'end'
-----------------------------------
This one is difficult to work out, it might require a check by hand.
Most of the others were incorrect residue numbering, weird residues
appearing out of nowhere, or the tags were in the wrong order, etc.
As I said, I will post a diff of these files to the originals once I
can handle them all. I have been modifying the files to fix them as I
go.
Regards,
Edward
On 1 February 2011 18:40, Eldon Ulrich<elu@xxxxxxxxxxxxx> wrote:
Hi,
I have found the data so there is no need to resend. We will look at how
best to get it into the entry.
Thanks,
Eldon
On 2/1/11 11:36 AM, Sébastien Morin wrote:
Hi guys,
I am currently looking up in my archives and I can't figure out what
happened...
I remember sending a lot of data to Hongyang Yao (hongyang at bmrb dot
wisc dot edu). I think these data were to be incorporated manually into
the entry since there was a change of version at the time which impeded
me to include the new data through the website.
The data included R1, R2, NOE (at 500, 600, and 800 MHz), order
parameters (S2), local correlation times (tau), amide exchange rates and
protection factors. These were all included in the entry.
The data also included Rex values and errors (scaled for 600 MHz), as
well as reduced spectral density values (J0, JwN, JwH at 500, 600 and
800 MHz). These seem all to be absent from the entry... Why I did not
notice at the time, I don't know... I was sure everything was in
place... but that's a long time ago...
If you need, Eldon, I could resend the files which contained the data
and were sent to Hongyang Yao...
Thanks a lot for help solving this issue, both for relax and for the
completeness of this BMRB entry...
Cheers,
Séb :)
On 11-02-01 6:24 PM, Eldon Ulrich wrote:
Hi,
The Rex data was deposited, but did not get incorporated into the
entry.
I am looking into this. I do not believe we had a separate save frame
for Rex data and this may be why it is not in the entry. I will be very
interested in the results of your parsing.
Eldon
On 2/1/11 10:29 AM, Edward d'Auvergne wrote:
Hi Seb,
I was just wondering if you had noticed that your 6838 BMRB deposition
was missing the Rex values and errors from the model-free saveframe?
Is it supposed to be like this? I'm not parsing the whole of the BMRB
model-free depositions from the BMRB-relax integration paper and
finding a lot of peculiarities/breakages. Eldon, I'll post some diffs
and explanations later, once I can parse it all.
Cheers,
Edward
Re: Missing Rex data from the bmr6838.str data file?