[Bioperl-pipeline] Re: is biopipeline able to work with v9 Ensembl API ?

[Andy Nunberg]

Yes,
There is no difference between that xml and the two files you just sent,
but it was not present in the original xml file you sent me..

I still need help with the blast problem, can anyone tell me what to look
at so that the blast does not go to standard out so that it maybe parsed??
Andy

At 09:43 AM 3/25/2003 +0800, you wrote:
>Hi Andy,
>
>I am sorry but I dont see the difference between this code and the xml 
>file that I have attached.....
>It caters for repeat masker and blast also.....
>
>Please let me know if the problem persists.....
>
>have a nice day
>regards
>
>bala
>
>
>
>
>On Tuesday, March 25, 2003, at 06:37  AM, Andy Nunberg wrote:
>
>> Bala,
>> playing with the xml file I am able to get sequences loaded,
>> I just added another method to the adapator 2
>> so it looks like this
>>
>>  <iohandler_setup>
>>     <iohandler id="1">
>>       <adaptor_id>2</adaptor_id>
>>       <adaptor_type>DB</adaptor_type>
>>       <iohandler_type>INPUT</iohandler_type>
>>       <method>
>> 	  	<name>get_RawContigAdaptor</name>
>> 		<rank>1</rank>
>> 		</method>
>> 	  <method>
>>         <name>get_all_Contig_id</name>
>>         <rank>2</rank>
>>        </method>
>>     </iohandler>
>>
>> Repeat masking looks good and the output is stored in the ens db.
>>
>> However, i am having problems with blast.
>> 1) i want to pass the argument -F 'm D' but this causes blast to crash 
>> and
>> in the exception all I see is
>> .... -F 'm
>> If i remove the -F argumen altogether then blast executes.
>> 2)When blast does execute, all the output is going to standard out 
>> instead
>> of to some file..
>> when I look in the ens DB, i dont see any dna or prot align features 
>> being
>> stored..
>>
>> Andy
>>
>> At 07:35 AM 3/24/2003 +0800, you wrote:
>>> Hi Andy,
>>>
>>>> It is still not working, should I keep using the template i was
>>>> modifying
>>>> in /dev or should I use the one you gave me?
>>>
>>> I feel that its better if you used the copy i sent you....
>>> Its tested already...so you can start using it....
>>> If you still have any problems do drop me a mail....
>>> we will brainstorm it together....
>>>
>>>
>>> regards
>>> bala
>>
>> *******************************************************************
>> Andy Nunberg, Ph.D
>> Computational Biologist
>> Orion Genomics, LLC
>> (314) 615-6989
>> http://www.oriongenomics.com
>>

*******************************************************************
Andy Nunberg, Ph.D
Computational Biologist
Orion Genomics, LLC 
(314) 615-6989
http://www.oriongenomics.com