[Bioperl-l] DB.t failures

Chris Fields cjfields at uiuc.edu
Thu Feb 15 10:44:23 EST 2007


On Feb 15, 2007, at 8:37 AM, Sendu Bala wrote:

> Chris Fields wrote:
>>
>> On Feb 15, 2007, at 7:37 AM, Sendu Bala wrote:
>>
>>> Jay Hannah wrote:
>>>> On Feb 14, 2007, at 8:02 AM, Sendu Bala wrote:
>>>>> DB.t is failing with BIOPERLDEBUG set. Apparently, we are no  
>>>>> longer
>>>>> getting sequences back from NCBI in the order we requested them in
>>>>> batch mode.
>>
>> Okay, I committed a fix for that.  I hope there are many users who
>> depend on the returned sequence order for anything!
>
> s/are/aren't/ ?

Yes, my oops.

> I suspect there might be, and its certainly a reasonable assumption to
> make. Did you not see an easy way of maintaining the order?

I haven't looked (been busy the last few days), but I think there is  
a way via efetch.

We could add in something to the default base URL if there is  
something or (probably better) add a sort_order() method to designate  
a particular sort order, defaulting to the old order if not set.

chris


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