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

Sun Apr 10 15:38:06 EDT 2005

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).%0ASKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGGYGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGRGFGGGSGSNFGGGGSYNDFGNYNNQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF&COMPOSITION_BASED_STATISTICS=off&EXPECT=1e-10&SERVICE=plain&FORMAT_OBJECT=Alignment&CMD=Put&FILTER=L&PROGRAM=blastp

<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 .