[Bioperl-l] RemoteBlast by Bio::Perl Through proxy

[CHANDAN SINGH]

Hi all 
As already mentioned i get error 500 while using Remoteblast through 
Bio::Perl module .Most of the time the error is 
500 Can't connect to www.ncbi.nlm.nih.gov:80 (connect: No route to host)
Sometimes the error is 
500 Can't connect to www.ncbi.nlm.nih.gov:80 (connect: timeout)
(refer to my first mail for details )

Of late I have been trying to trace out the bug and found that 
The subroutine    UserAgent ::_need_proxy         returns an undef value 
in my case .
I would like to know more about this  subroutine and request all who
know about it to please respond .
Thanks 
Chandan

On 4/13/05, Madeleine Lemieux <mlemieux at bioinfo.ca> wrote:
> Chandan,
> 
> In your own best interest, you should post your responses to the list.
> That way you get the benefit of a large talent pool rather than
> limiting yourself to what little I know.
> 
> You can try getting a fresh copy of RemoteBlast.pm from the bioperl
> website just in case you unintentionally changed something other than
> that one line.
> 
> But it seems to me as if you're timing out before the NCBI server has
> time to respond in which case I'm afraid I don't know how to help you.
> If you do traceroute www.ncbi.nlm.nih.gov, do you reach the server in a
> reasonable amount of time?
> 
> Madeleine
> 
> > hi Madeleine Lemieux
> > Thanks for ur reply . Yes the error  happens everytime i run the code
> > and you deduced correctly that the get_sequence works
> > fine . Yes i did try to appened one line to RemoteBlast after making
> > a few attempts to run the code but it did not work and i removed it .
> > Do you suggest installing the modules again ?
> >
> > chandan
> >
> > On Apr 12, 2005 3:55 AM, Madeleine Lemieux <mlemieux at bioinfo.ca> wrote:
> >> Chandan,
> >>
> >> Does this error happen every time you run the code? The get_sequence
> >> works otherwise your error message would have come from EBI, not NCBI,
> >> which means your proxy is set up OK. Both get_sequence and
> >> blast_sequence eventually call the same User Agent code so if one
> >> works, the other should as well. Have you edited either Perl.pm or
> >> RemoteBlast.pm?
> >>
> >> Madeleine
> >>
> >>> I am a newbie and while installing bioperl and other related softwres
> >>> i had installation problems
> >>> but fortunately succeeded in debugging few .I had no idea where to
> >>> share those experiences
> >>> but now being  a member of this forum might help. Though i dont have
> >>> the installation outputs
> >>> i would like to share the last such experience  while installind
> >>> Berkeley DB .It was not able to include a file Extern.h and i found
> >>> that the concerned file in
> >>> /usr/lib/perl5/..../Core/Extern had a wrong extension . After setting
> >>> it to Extern.h installation was
> >>> possible.I could not install few other related softwares .
> >>>
> >>> At present i am facing this problem.The second code for blast in
> >>> bptutorial(html format on bioperl site ) when run does not yield the
> >>> desired result .
> >>> #! /usr/bin/perl
> >>>  use Bio::Perl;
> >>>  $seq_object = get_sequence('swiss',"ROA1_HUMAN");
> >>>     # uses  the default database - nr in this case
> >>>        $blast_result = blast_sequence($seq_object);
> >>>
> >>>            write_blast(">roa1.blast",$blast_result);
> >>> The output after running the code is
> >>> ------------------- WARNING ---------------------
> >>> MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
> >>> User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.5
> >>> Content-Length: 651
> >>> Content-Type: application/x-www-form-urlencoded
> >>>
> >>> DATABASE=nr&QUERY=%3EROA1_HUMAN+Heterogeneous+nuclear+ribonucleoprote
> >>> in
> >>> +A1+(Helix-destabilizing+protein)+(Single-
> >>> strand+binding+protein)+(hnRNP+core+protein+A1).%0ASKSESPKEPEQLRKLFIG
> >>> GL
> >>> SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAV
> >>> SR
> >>> EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDK
> >>> IV
> >>> IQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSR
> >>> GG
> >>> GGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGGSG
> >>> SN
> >>> FGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF&C
> >>> OM
> >>> POSITION_BASED_STATISTICS=off&EXPECT=1e
> >>> -10&SERVICE=plain&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&PROGRAM=bl
> >>> as
> >>> tp
> >>>
> >>> <HTML>
> >>> <HEAD><TITLE>An Error Occurred</TITLE></HEAD>
> >>> <BODY>
> >>> <H1>An Error Occurred</H1>
> >>> 500 Can't connect to www.ncbi.nlm.nih.gov:80 (connect: No route to
> >>> host)
> >>> </BODY>
> >>> </HTML>
> >>>
> >>> ---------------------------------------------------
> >>> Submitted Blast for [ROA1_HUMAN]
> >>>
> >>>
> >>> The env variable HTTP_PROXY or /and http_proxy is set correct .I hope
> >>> somebody can
> >>> help me out .
> >>> Thank You .
> >>
> >> _______________________________________________
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> >> Bioperl-l at portal.open-bio.org
> >> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> 
>