[Bioperl-l] starter..help run the first script

Sendu Bala bix at sendu.me.uk
Thu Aug 17 04:56:47 EDT 2006


Reena Yadav wrote:
> Hi I am a novice and am seriously starting today.
> I tried the following script, put in a text editor and saved it as  .pl as
> ext.
> Internet is connected, Web proxy is set. But is not recognised by the
> script.
> Could someone walk me through how exactly to write, save, and run the script
> in Linux or win, preferably linux.
> Reena Yadav
> SCRIPT
> ----------
> #!/usr/bin/perl -w
> use Bio::Perl;
> 
> # this script will only work if you have an internet connection on the
> # computer you're using, the databases you can get sequences from
> # are 'swiss', 'genbank', 'genpept', 'embl', and 'refseq'
> 
> $seq_object = get_sequence('swiss',"ROA1_HUMAN");
> 
> write_sequence(">roa1.fasta",'fasta',$seq_object);

[...]

> <H3>This site is protected by firewall 126.
> All requests are screened and logged.</H3><P>
> 
> <H2>You are not permitted to access the requested URL
> http://www.ebi.ac.uk/cgi-bin/dbfetch.</H2><P>
> 
> <HR>
> <center>
> <H4>For further information contact:
> <ADDRESS>TP&amp;S Firewall
> Admin, Wilmington</ADDRESS></H4>

Your script is running fine. As you can see from the error message, your 
web proxy firewall is not allowing you to access the ebi website (can 
you visit http://www.ebi.ac.uk/cgi-bin/dbfetch in a web browser on the 
same machine?). You'll need to get in touch with the 'firewall admin', 
or change web proxy.


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