[Bioperl-l] remoteblast xml problem

Sendu Bala sb at mrc-dunn.cam.ac.uk
Fri Jun 2 05:04:18 EDT 2006


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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