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

[CHANDAN SINGH]

Hi to all 
I found a reason because of which get_sequence works and
blast_sequence does not .
The  fact is that for "Bio::Perl::blast_sequence " the subroutine 
LWP::UserAgent::env_proxy() is not called while for Bio::Perl::get_sequence
it is called and so Bio::Perl::get_sequence works fine . 
I have run two more programs and am 100% sure of what i'm talking 
about .
I will be very thankful if somebody could help me out .
Thanks in advance .
Chandan

On 4/14/05, CHANDAN SINGH <chandan.kr.singh at gmail.com> wrote:
> 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 .
> > >>
> > >> _______________________________________________
> > >> Bioperl-l mailing list
> > >> Bioperl-l at portal.open-bio.org
> > >> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >>
> > >
> >
> >
>