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

Tue Apr 12 20:08:44 EDT 2005

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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>