Hi,
I had installed fresh Python2.4 and other required packages and tested the
full version of megatest again. The error still exists.
The error is when we query full chromosome in NLMSA, it gives fake results.
i.e. if we expect 100 results for chrY, it gives 105 results and 5 are fake
results. I checked those things and found out that it has different
chromosome location from text input files.
If you check annotation_hg18_megatest.py, you can see "sys.exit('wrong
query')". The reason why I put this into this code is that pygr should NOT
return slice object with NEGATIVE coordinates. But, some of NLMSA results
falled into this part if you run megatest in Python2.4 and latest Pyrex.
This script works very nicely when I made megatest, two years ago, Python2.4
and Pyrex downloaded at that time.
This error may not be the problem with the megatest, but it would be the
problem with Python2.4 + latest Pyrex.
Python2.5 + latest Pyrex works very well for all full version of megatest.
Yours,
Namshin Kim
On Thu, Jul 16, 2009 at 10:02 AM, Namshin Kim <[email protected]> wrote:
> Hi Chris, Marek,
> I think the python already installed (/usr/bin/python) in llpygr may have
> the problem. How about installing fresh version of python from source and
> then do the megatest?
>
> Namshin Kim
>
>
> On Thu, Jul 16, 2009 at 9:57 AM, Christopher Lee <[email protected]>wrote:
>
>>
>> Hi Marek, Namshin,
>> like any test suite, the megatests are supposed to run successfully on
>> all platforms that Pygr supports, so that we can use them to test Pygr
>> on all those platforms. It doesn't make sense to tie the megatest
>> code to a specific Python version.
>>
>> -- Chris
>>
>>
>> On Jul 15, 2009, at 5:51 PM, Marek Szuba wrote:
>>
>> > On Thu, 16 Jul 2009 09:43:10 +0900
>> > Namshin Kim <[email protected]> wrote:
>> >
>> >> As I already mentioned, the python installed in llpygr should be
>> >> replaced with latest version, Python 2.5.4. and all other packages.
>> > This is one thing that needs discussing. Chris, do you think it's okay
>> > for megatests to be tied to a specific Python version? Namshin, can
>> > you tell whether using the same Python version on a different platform
>> > (i.e. not Linux/amd64) would allow megatests to run successfully or
>> > not?
>>
>> >>
>>
>
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