[Bioperl-l] remoteblast xml problem

Chris Fields cjfields at uiuc.edu
Fri Jun 2 17:54:20 EDT 2006


Hubert, 

Could you post this on bugzilla with your script and test data so I can try
to replicate you error?  I may not get to it until Monday.

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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