System Code Error

[Soon Sen]

Dear GenMAPP Users,

I tried running the GO-Elite program (1.2.3-Win32) on my Windows XP
computer. The database I tried using is the Mus Musculus EnsMart62Plus
database, with Ensembl as the MOD primary relational database. I have
put in MGI IDs as gene identifiers in the input file. The gene ID and
system code columns for the first five genes in the denominator file
are as shown below:-

MGI:101757 M
MGI:101758 M
MGI:101759 M
MGI:101760 M
MGI:101761 M

However, an error occurred during the analysis with a pop-up message
as follows:-

WARNING!!! NO gene SystemCode identified in: file1.txt
Please provide in input text file and re-run
If SystemCode column present, the file format may be incorrect

The log file displays the following message:-

Traceback (most recent call last):
File "GO_Elite.py", line 2212, in <module>
File "GO_Elite.py", line 1645, in write
File "GO_Elite.py", line 1646, in set
File "Tkinter.pyc", line 911, in update
_tkinter.TclError: can't invoke "update" command: application has
been destroyed

Not sure what is the error here, as I think MGI IDs are supported in
the database used?

Thank you,
Leow.

[GenMAPP]

Hi Soon,

This is a very interesting error. I found that it occurs
because there are two MGI tables in the database:
Ensembl-MGI
Ensembl-MGI_transcript_name

The current version of GO-Elite searches for a file that
contains the name Ensembl-MGI and is choosing the latter
rather than the first file. I think Ensembl introduced
these new tables recently, so this wouldn't have been a
problem in earlier databases. To fix right now, simply
delete the file "Ensembl-MGI_transcript_name" from the
GO-Elite/Databases/EnsMart62Plus/uid-gene/. I will do the
same for the web-service. I will make sure this is fixed
in 1.2.4.

Best,
Nathan

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