[Bioperl-l] more question regarding RemoteBlast.pm version 1.28

Guojun Yang gyang at plantbio.uga.edu
Fri Feb 3 19:44:50 UTC 2006

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,  

Department of Plant Biology
University of Georgia
Tel: 706-542-1857
Fax: 706-542-1805

  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


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

while ( my @rids = $factory->each_rid ) {
foreach my $rid ( @rids ) {
my $rc = $factory->retrieve_blast($rid);
if( !ref($rc) ) {
if( $rc < 0 ) {
print STDERR "." if ( $v > 0 );
sleep 5;
} else { # parsing
starts here
my $result = $rc->next_result(); # it should hang
#save the output
my $filename = $result->query_name()."\.out";
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
> >
> >
> >
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> Bioperl-l at lists.open-bio.org
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