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Fails to load Genbank accession NC_000913.2

description

Hi,
 
Very nice program. When I try to load the Genbank record for E. coli K-12 MG1655 (attached) the program crashes.
 
Vince

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kajaldas007 wrote Aug 25, 2011 at 8:04 PM

Hi,
First of all, thanks for trying out the application and providing feedback.

If you are testing the application with extreme boundary conditions, then it's ok. Else, I would like to make the following points:
  1. The file is not valid because it doesn't contain the sequence itself. In fact, this is where the parser is getting stuck. I ran the mbf code in debug mode with this file and observed that mbf parser is reading the header and feature data correctly. Then it is reaching the end of the file where it is finding only "ORIGIN" tag followed by nothing. The parser is expecting the sequence data there.
  2. It's sad that the mbf is parser is not handling this exception scenario and throwing any meaningful exception. As a result, even if I handle the exception in my program, I am not getting any useful information. The exception is null reference exception. I will report it to Microsoft.
  3. Anyway, I will handle the exception so that the program doesn't crash.
Finally, try the program with some valid file (preferably not too large file, as still some work needs to be done on the UI performance) and enjoy!

Thanks
Kajal

vforget wrote Aug 25, 2011 at 10:14 PM

Hi Kajal,

Thanks for the quick reply. It was an accidental test of boundary conditions (didn't realize the record was missing the sequence), but also something I thought would be realistic (inspecting the annotations from a complete bacterial genome).

I'll try with a smaller file, but also with NC_000913.2, and report any UI issues back to you.

Vince

wrote Feb 13, 2013 at 8:22 PM