mailRe: Data set format


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Posted by Gary Thompson on August 30, 2007 - 11:57:
Hi,

Sorry, would you be able to resend your message?  It was only sent to
me and not Seb or the mailing list.

Cheers,

Edward


On 8/28/07, gary thompson <garyt.and.sarahb@xxxxxxxxx> wrote:
Dear Seb

The things (I think ;-)) that are generally needed are
1. we should fail quickly if something is wrong
2. the failure message should have
   a. a filename  with a complete path
   b. a line number and a field number
   c. the line itself with the error indicated

error failed to read data from wobble.txt, bad data format!
file: /wibble/wobble.txt had an integer at line 56 column 6 when it should
be a string
1 2 3 b a 6 ...

3. The things to check for are
   a. correct number of arguments
   b. the correct type for arguments

allowing comments in these files is also a good idea that i looked at at one
point

specifically this allows

a. the user (or program) to record meta information abou the file
b. would allow files such as the monte carlo outputs to have meta
information to allow the human reader to more easily distinguish the
sections in the file

any way there are some off the cuff thoughts

regards
gary




On 8/27/07, Edward d'Auvergne < edward.dauvergne@xxxxxxxxx> wrote:
>
> Hi,
>
> For the reading in of data, such as the R1 relaxation rates, the only
> requirement for the format is that the data is in a column formatted
> text file.  The different columns can be changed by the num_col=0,
> name_col=1, data_col=2, and error_col=3 arguments.  The column
> separator changed by the 'sep' argument.  In the future, even more
> diverse formats will be accepted as these arise and are reported on
> the mailing lists.
>
> With this in mind, coming up with a more descriptive error message
> would be worthwhile.  Currently you will get something such as:
>
> RelaxError:  "The relaxation data is invalid (num=" +
> file_data[i][num_col] + ", name=" + file_data[i][name_col] + ", data="
> + file_data[i][data_col] + ", error=" + file_data[i][error_col] + ")."
>
> This could probably be broken into simpler messages for different
> types of error.  The checks are currently for the residue number being
> an integer, and the data and error being floating point numbers.
> Would anyone have any suggestions or ideas for how this could be
> better reported to the user?  What tests and what types of messages
> would you use?  The system has to be flexible enough to handle
> absolutely all rubbish thrown at it by a user ;)
>
> Cheers,
>
> Edward
>
>
>
> On 8/21/07, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
> > Hi all !
> >
> > I am now analysing data using relax (line 1.2, branch consistency-tests,
> > revision 3354).
> >
> > I realized (when using the consistency tests function) that it could be
> > nice to check data set format and output a error message when the format
> > isn't like the one requested.
> >
> > For example, a data set of the following format wouldn't work :
> >
> > 1 0.90 0.05
> > 2 0.79 0.05
> > 3 0.6  0.1
> >
> > neither would it work with the following format :
> >
> > Gly  1  0.90  0.05
> > Gly  2  0.79  0.05
> > Gly  3  0.6    0.1
> >
> >
> > However, a dataset of the following format would work as it is the
> > format required :
> >
> > 1  Gly   0.90  0.05
> > 2  Gly  0.79  0.05
> > 3  Gly  0.6    0.1
> >
> >
> > This type of error is long to find out for a standard user as the error
> > messages yielded are not very helpful.
> >
> > So, would it be a good idea to add a kind of test for the data set
> > format ? Maybe this has been already proposed for the 1.3 line. If so,
> > sorry for the duplicate request...
> >
> > Cheers !
> >
> >
> > Sébastien  :)
> >
> > --
> >          ______________________________________
> >      _______________________________________________
> >     |                                               |
> >    || Sebastien Morin                               ||
> >   ||| Etudiant au PhD en biochimie                  |||
> >  |||| Laboratoire de resonance magnetique nucleaire ||||
> > ||||| Dr Stephane Gagne
|||||
> >  |||| CREFSIP (Universite Laval, Quebec, CANADA)    ||||
> >   ||| 1-418-656-2131 #4530                          |||
> >    ||                                               ||
> >     |_______________________________________________|
> >          ______________________________________
> >
> >
> >
> > _______________________________________________
> > relax (http://nmr-relax.com)
> >
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