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 |||
|| ||
|_______________________________________________|
______________________________________
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Re: Data set format