[Bioperl-l] more on RemoteBlast.pm version 1.28

Guojun Yang gyang at plantbio.uga.edu
Mon Feb 13 13:32:14 EST 2006


Hi, Chris,  
I do have different versions of bioperl on my Linux machine (1.4. and 1.5.0), this may be the problem. Should I just install bioperl-1.5.1 or I need to uninstall and remove the previous versions. I could not find any hint on uninstalling bioperl on linux. Could you please give me some suggestion?  
Thanks,  
Guojun

Department of Plant Biology
University of Georgia
      _____  

  From: Chris Fields [mailto:cjfields at uiuc.edu]
To: gyang at plantbio.uga.edu, bioperl-l at lists.open-bio.org
Sent: Mon, 13 Feb 2006 11:45:14 -0500
Subject: RE: [Bioperl-l] more question regarding RemoteBlast.pm version 1.28

  
  
If you’re using RemoteBlast 1.28, then you’ve likely updated from CVS which isn’t the latest fix.    
   
Make sure that you check the following:   
   
1) Always post to the mailing list: http://www.bioperl.org/wiki/HOWTO:Beginners#Getting_Assistance .    
   
2) You must have the complete bioperl-1.5.1 or bioperl-live (CVS) installed first.  Perform a clean installation; do not upgrade only Bio::SearchIO::blast and Bio::Tools::Run::RemoteBlast, as we can't guarantee that mixing modules from old and new distributions (1.4 and 1.5.1, for instance) will work.  A bioperl-1.5.1 or bioperl-live installation will allow text output from BLAST v.2.2.12 to be saved and parsed; it will not parse the newest BLAST text output from NCBI (v2.2.13) but it should still save it. I believe as long as next_results() isn’t called, it will work.  
   
3) The bug fixes for the above issue with parsing BLAST 2.2.13 text output are NOT in CVS; they haven’t been cleared and checked in by Roger Hall (who’s now taking care of RemoteBlast) and the powers that be (Jason or whomever is in charge of Bio::SearchIO).  They can be found in Bugzilla:  
   
http://bugzilla.bioperl.org/show_bug.cgi?id=1934  
http://bugzilla.bioperl.org/show_bug.cgi?id=1935  
   
The fix in RemoteBlast in Bugzilla (#1935) is to allow the option of saving XML output, so isn’t necessary if you don’t plan on using this option.  And, remember, they haven’t been committed yet to CVS, which means that the final version will change to refle the new version.  
  

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign   
  
  
    _____  

    
From: Guojun Yang [mailto:gyang at plantbio.uga.edu] 
Sent: Monday, February 13, 2006 9:26 AM
To: Chris Fields
Subject: RE: [Bioperl-l] more question regarding RemoteBlast.pm version 1.28  
   
  
Hi, Chris  
  
Thanks for your suggestion, however, it doesn't seem to work for my cgi even after I replace both blast.pm and RemoteBlast.pm. I didn't even get any RID. Is there any suggestion?  
  
   
  
Guojun  


Guojun Yang
Department of Plant Biology
University of Georgia
Tel: 706-542-1857
Fax: 706-542-1805
http://www.arches.uga.edu/~guojun  
    _____  

    
From: Chris Fields [mailto:cjfields at uiuc.edu]
To: gyang at plantbio.uga.edu, bioperl-l at bioperl.org
Sent: Fri, 03 Feb 2006 16:07:29 -0500
Subject: RE: [Bioperl-l] more question regarding RemoteBlast.pm version 1.28

I would say give the new code a try, but realize that it hasn't been checked
in (like I said below). I will try going over the modified
Bio::SearchIO::blast again this weekend to see if there is anything I might
have missed. The changed order in the header of BLAST text output has me a
bit worried that it might not catch everything, but it at least doesn't hang
in the while() loop I described in the bug report below (bug #1934) and
seems to process everything fine.

If you want more stability in the code, you might consider changing over to
XML output and parsing with Bio::SearchIO::blastxml. There are some changes
in Bio::Tools::Run::RemoteBlast (bug #1935) that accommodate saving XML
output, but I believe it parses everything regardless. If you look back the
last month or so there has been a bit of discussion here about it. Jason
describes a bit on how to set up RemoteBlast for XML:

http://bioperl.org/news/2005/11/06/getting-blastxml-using-remoteblast/

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Guojun Yang
> Sent: Friday, February 03, 2006 1:45 PM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] more question regarding RemoteBlast.pm version 1.28
> 
> Hi, Everybody,
> I see this post and am wondering if this is the reason for the
> malfunctionning of my webserver. We set up a webserver named MAK, for MITE
> sequence analysis. It was working very well until around November 2005,
> when it stopped returning any result (the site is fine and seems to be
> doing sth after submission). In the CGI script, I used remoteblast (that
> work was done in 2003) to do searches. I currently do not have access to
> the server because I moved. Quite several people sent emails to us about
> its malfunctioning. Is there any suggestion on fixing the problem? Should
> I simplily ask the remoteblast.pm be replaced with the new version?
> Thanks a lot,
> Guojun
> 
> Department of Plant Biology
> University of Georgia
> Tel: 706-542-1857
> Fax: 706-542-1805
> http://www.arches.uga.edu/~guojun
> _____
> 
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> To: 'Nagesh Chakka' [mailto:nagesh.chakka at anu.edu.au], 'Huang Jian'
> [mailto:hjian at kuicr.kyoto-u.ac.jp], 'bioperl-l' [mailto:bioperl-
> l at bioperl.org]
> Sent: Fri, 03 Feb 2006 10:45:23 -0500
> Subject: Re: [Bioperl-l] RemoteBlast.pm version 1.28
> 
> Like Nagesh says, try the latest RemoteBlast from bioperl-live CVS. It
> will
> work for saving text output. However, it will not parse anything using
> next_result (it will likely hang) and will not save XML format. See these
> bugs:
> 
> http://bugzilla.bioperl.org/show_bug.cgi?id=1934
> http://bugzilla.bioperl.org/show_bug.cgi?id=1935
> 
> for explanations and possible fixes (changes to RemoteBlast and
> Bio::SearchIO::blast). Note that these haven't been checked in yet so are
> still not included in bioperl-live; they may be further modified before
> committing to CVS. If you're not worried about XML, you could just try the
> first fix, which is a change to SearchIO::blast.
> 
> Nagesh, I remember you posting to the list a month ago using a script
> which
> had problems; the script you used saves the output but doesn't actually
> parse it (i.e. you don't use next_result() to go through the data). Is the
> version of BLAST in your text output 2.2.12 or 2.2.13? Have you tried
> parsing the output using "-readmethod => SearchIO" or "-readmethod =>
> blast"
> using your version of RemoteBlast and method next_result()? Like below
> (from
> perldoc):
> 
> while ( my @rids = $factory->each_rid ) {
> foreach my $rid ( @rids ) {
> my $rc = $factory->retrieve_blast($rid);
> if( !ref($rc) ) {
> if( $rc < 0 ) {
> $factory->remove_rid($rid);
> }
> print STDERR "." if ( $v > 0 );
> sleep 5;
> } else { # parsing
> starts here
> my $result = $rc->next_result(); # it should hang
> here
> #save the output
> my $filename = $result->query_name()."\.out";
> $factory->save_output($filename);
> $factory->remove_rid($rid);
> print "\nQuery Name: ", $result->query_name(), "\n";
> while ( my $hit = $result->next_hit ) {
> next unless ( $v > 0);
> print "\thit name is ", $hit->name, "\n";
> while( my $hsp = $hit->next_hsp ) {
> print "\t\tscore is ", $hsp->score, "\n";
> }
> }
> }
> }
> }
> }
> 
> 
> My script hanged if I used next_result() in any way prior to the fixes. I
> want to see how many others are having the same issues with parsing using
> the CVS version of bioperl-live.
> 
> Christopher Fields
> Postdoctoral Researcher - Switzer Lab
> Dept. of Biochemistry
> University of Illinois Urbana-Champaign
> 
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Nagesh Chakka
> > Sent: Thursday, February 02, 2006 7:24 PM
> > To: Huang Jian; bioperl-l
> > Subject: Re: [Bioperl-l] RemoteBlast.pm version 1.28
> >
> > Hi Huang,
> > Thanks for the message. The older version of RemoteBlast.pm works on the
> > logic of checking the temporary file size to determine whether the Blast
> > results are ready. This condition is not getting satisfied may be due to
> > some changes brought about by NCBI. I had this problem recently and
> > figured out that the solution was to use the latest version which has
> > this problem fixed (does not use file size logic any more) which is not
> > yet included in the BioPerl package.
> > Cheers
> > Nagesh
> >
> > Huang Jian wrote:
> >
> > > Dear Nagesh,
> > >
> > > I have replaced my old RemoteBlast.pm (v 1.17) with v 1.28 you send
> > > me. Now it works perfectly!!!
> > >
> > > Thank you!!
> > >
> > > Huang
> > >
> > > ----- Original Message ----- From: "Nagesh Chakka"
> > > <nagesh.chakka at anu.edu.au>
> > > To: "Huang Jian" <hjian at kuicr.kyoto-u.ac.jp>; "bioperl-l"
> > > <bioperl-l at bioperl.org>
> > > Sent: Friday, February 03, 2006 7:48 AM
> > > Subject: Re: [Bioperl-l] Sorry, failure in post on the net, so still
> > > via email
> > >
> > >
> > >> Hi Huang,
> > >> I see that you are submitting a sequence for a remote blast search.
> Can
> > >> you check if the RemoteBlast.pm being used is v 1.28 (2005/12/09). If
> > >> not I have attached it with this email, try to replace it with the
> old
> > >> one which has a bug.
> > >> Let me know if it works.
> > >> Nagesh
> > >
> > >
> > >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
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> 
> 
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