[Bioperl-l] 2 questions about Bio::Tools::WebBlat

Phil- phil511 at 21cn.com
Mon Jan 23 11:41:23 EST 2006


Greetings, everyone!

	I'm an undergraduate from Sun Yat-Sen University of China. I am currently using bioperl to map some of my cDNA sequences onto human chromosomes. I used the Bio::Tools::WebBlat but something just goes wrong. Here comes my code:

      BEGIN{$ENV{HTTP_PROXY}='http://202.116.64.1:8001/';}

      use Bio::Tools::WebBlat;
      use Bio::Seq;

      my $webblat = Bio::Tools::WebBlat->new();
      my $seq = Bio::Seq->new(-id => 'foo' , -seq => 'aataataat' );
      my $searchio = $webblat->create_searchio(sequence=>$seq);

      while(my $result = $searchio->next_result){
        sleep 1;
      }

	As you can see that I have to use a proxy. But i can't get the results by these codes. I further check the result of the LWP::UserAgent->request called inside WebBlat.pm and I think I found a mistake at the last line of code:

      $self->throw($ua->status_line);

   I think status_line should be a method of HTTP::Response but not LWP::UserAgent. I change the code and what I got is a '500 Internal Server Error', and with the following lines:

----------------------------
The page you requested resulted in a server problem on our systems.

We hate this type of error immensely and we're sure that you do as well. While we have logged it and rapidly pursue any problems on our systems,sometimes extra information from the user can pinpoint the cause of the problem for us and help us prevent it in the future. If you have information that you would like to provide about what led to the error, please email us at genome-www at soe.ucsc.edu.

If you are unable to access commonly-used features on our website, it is possible that you may need to reset your Genome Browser with the following URL: http://genome.ucsc.edu/cgi-bin/cartReset. This will replace your stored settings with the default configuration and will return your Browser to the state it was in when you first accessed it.

We apologize for the inconvenience. 
----------------------------

It seems that my script get contact with UCSC server but can't work though to get the result. What should I do? Thank you all!
 				

¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Phil-
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡phil511 at 21cn.com
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2006-01-24



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