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

Mon Apr 11 18:25:46 EDT 2005

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+ribonucleoprotein 
> +A1+(Helix-destabilizing+protein)+(Single- 
> strand+binding+protein)+(hnRNP+core+protein+A1).%0ASKSESPKEPEQLRKLFIGGL 
> SFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSR 
> EDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 
> IQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGG 
> GGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGGSGSN 
> FGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF&COM 
> POSITION_BASED_STATISTICS=off&EXPECT=1e 
> -10&SERVICE=plain&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&PROGRAM=blas 
> 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 .