[Bioperl-l] remoteblast xml problem

Hubert Prielinger hubert.prielinger at gmx.at
Fri Jun 2 19:19:40 EDT 2006


hi,
I have submitted the bug -> Bug 2017
with the script and input file, just start it from command line

thank you very much
greetings

Hubert

Chris Fields wrote:
> Hubert,
>
> I have a script that's using blastxml and XML output which seems to work.
> I'll try looking at it to get a better idea this weekend.
>
> Chris
>
>   
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Hubert Prielinger
>> Sent: Friday, June 02, 2006 4:12 PM
>> To: Chris Fields; bioperl-l at bioperl.org; Chris Fields; 'Sendu Bala'
>> Subject: Re: [Bioperl-l] remoteblast xml problem
>>
>> hi,
>> sorry, but I have updated the remoteblast module and I have run several
>> attempts with the same results as before. It didn't work.
>> I didn't get any results.
>>
>> regards
>> Hubert
>>
>>
>> Chris Fields wrote:
>>     
>>> Sendu, Hubert,
>>>
>>>
>>> Hubert, your code looks fine so Sendu's patch should fix the problem
>>>       
>> (break
>>     
>>> out of that infinite loop).  I applied Sendu's patch to RemoteBlast in
>>>       
>> CVS;
>>     
>>> it passed all tests in RemoteBlast.t.  Try updating from CVS to see if
>>>       
>> it
>>     
>>> works.
>>>
>>> Chris
>>>
>>>
>>>       
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>>>> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
>>>> Sent: Friday, June 02, 2006 4:04 AM
>>>> To: bioperl-l at lists.open-bio.org
>>>> Subject: Re: [Bioperl-l] remoteblast xml problem
>>>>
>>>> Hubert Prielinger wrote:
>>>>
>>>>         
>>>>> hi,
>>>>> I have the following program and it worked quite well, for retrieving
>>>>> remoteblast results in a textfile,
>>>>> now I have altered it to to xml, and it didn't work anymore.....
>>>>> it takes all the parameter at the commandline, submits the query, but
>>>>>           
>> I
>>     
>>>>> don't retrieve any results file anymore.....
>>>>>
>>>>> it seems that it hangs in a endless loop......
>>>>> the only output I get is:  $rc is not a ref! over and over..... it
>>>>> doesn't enter the else term anymore....
>>>>>
>>>>>           
>>>> There is no problem with your code. The problem is with the NCBI server
>>>> and should be reported to them. You can visit the site and do a blast,
>>>> requesting xml format, and you will typically get one normal 'waiting'
>>>> message and the promise that it will be updated in x seconds, but
>>>> subsequent attempts to get progress information result in an xml error
>>>> page because the NCBI server doesn't actually send any data.
>>>>
>>>> Unfortunately the way that the bioperl code is written, it treats no
>>>> data as 'waiting' instead of an error. I've offered a patch to fix this
>>>> at this bug page:
>>>> http://bugzilla.bioperl.org/show_bug.cgi?id=2015
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>>>>
>>>>         
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>>>
>>>
>>>       
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>
>
>   



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