[gt-users] warnings

[Sascha Steinbiss]

On 01/05/2010 06:21 PM, Brent Pedersen wrote:
> hi,

Hi Brent,

> how can i turn off warnings from within python.
> when i do:
> 
> import gt
> f = gt.FeatureIndexMemory()
> f.add_gff3file("some.gff")
> 
> it gives the warnings about:
> warning: seqid "2" on line 2 in file "some.gff" has not been
> previously introduced with a "##sequence-region" line, create such a
> line automatically

I just added support for toggling this from Python (from C it's
trivial). From now on, you can just use gt.warning_disable().
My test case was:

  #!/usr/bin/python
  import gt
  import sys
  f = gt.FeatureIndexMemory()
  print "disabling warnings"
  gt.warning_disable()
  f.add_gff3file((sys.argv)[1])
  print "re-enabling warnings"
  gt.warning_enable_default()
  f.add_gff3file((sys.argv)[1])

and it worked:

$ ./testwarn.py ../../gt_stuff/user_examples/example.gff3
disabling warnings
re-enabling warnings
warning: skipping blank line 13 in file
"../../gt_stuff/user_examples/example.gff3"
$

The new code is in the git master or the unstable tarball.

> i also made the change pasted below to stop problems (segfaults) i was
> having when running under modwsgi/apache:
[snip]

Thanks a lot. I will have a look at that and integrate it (though I do
not really get what is fundamentally different now compared to the old
code).

Sascha

-- 
Sascha Steinbiss
Center for Bioinformatics
University of Hamburg
Bundesstr. 43
20146 Hamburg
Germany

Email:  steinbiss at zbh.uni-hamburg.de
URL:    http://www.zbh.uni-hamburg.de/steinbiss
Phone:  +49 (40) 42838 7322
FAX:    +49 (40) 42838 7312