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

Reena Yadav reenayadav at gmail.com
Thu Aug 17 03:00:50 EDT 2006


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);

REPLY ON THE PAGE
------------------------

------------- EXCEPTION  -------------
MSG: WebDBSeqI Request Error:
HTTP/1.1 403 Forbidden
Connection: close
Date: Thursday, 17-Aug-06 06:31:28 GMT
Server: Web_Proxy
Content-Type: text/html
Expires: Thursday, 17-Aug-06 06:31:28 GMT
Client-Date: Thu, 17 Aug 2006 12:01:10 GMT
Client-Peer: 193.62.197.151:80
Client-Response-Num: 1
Title: Web Proxy

<HTML>
<TITLE>Web Proxy</TITLE>
<HR>
<H1>Web Proxy</H1>
<HR>

<H3>This site is protected by firewall 126.
[ryadav at inbgsc0125 ~/ry_files]$ perl bt2.pl
Name "main::sequence_as_a_string" used only once: possible typo at
bt2.plline 22.
Use of uninitialized value in concatenation (.) or string at
/usr/lib/perl5/site_perl/5.8.5/Bio/Perl.pm line 169.
read_sequence() - usage incorrect at
/usr/lib/perl5/site_perl/5.8.5/Bio/Perl.pm line 168
        Bio::Perl::read_sequence('undef') called at bt2.pl line 5
[ryadav at inbgsc0125 ~/ry_files]$ perl bt1.pl

------------- EXCEPTION  -------------
MSG: WebDBSeqI Request Error:
HTTP/1.1 403 Forbidden
Connection: close
Date: Thursday, 17-Aug-06 06:43:03 GMT
Server: Web_Proxy
Content-Type: text/html
Expires: Thursday, 17-Aug-06 06:43:03 GMT
Client-Date: Thu, 17 Aug 2006 12:12:45 GMT
Client-Peer: 193.62.197.151:80
Client-Response-Num: 1
Title: Web Proxy

<HTML>
<TITLE>Web Proxy</TITLE>
<HR>
<H1>Web Proxy</H1>
<HR>

<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>
</center>
</HTML>

STACK Bio::DB::WebDBSeqI::_stream_request
/usr/lib/perl5/site_perl/5.8.5/Bio/DB/WebDBSeqI.pm:728
STACK Bio::DB::WebDBSeqI::get_seq_stream
/usr/lib/perl5/site_perl/5.8.5/Bio/DB/WebDBSeqI.pm:460
STACK Bio::DB::WebDBSeqI::get_Stream_by_id
/usr/lib/perl5/site_perl/5.8.5/Bio/DB/WebDBSeqI.pm:287
STACK Bio::DB::WebDBSeqI::get_Seq_by_id
/usr/lib/perl5/site_perl/5.8.5/Bio/DB/WebDBSeqI.pm:153
STACK Bio::Perl::get_sequence /usr/lib/perl5/site_perl/5.8.5/Bio/Perl.pm:511
STACK toplevel bt1.pl:8

--------------------------------------

-------------------- WARNING ---------------------
MSG: id (ROA1_HUMAN) does not exist
---------------------------------------------------
Use of uninitialized value in length at
/usr/lib/perl5/site_perl/5.8.5/Bio/Perl.pm line 271.
Use of uninitialized value in concatenation (.) or string at
/usr/lib/perl5/site_perl/5.8.5/Bio/Perl.pm line 283.
You have a non object [] passed to write_sequence. It maybe that you want to
use new_sequence to make this string into a sequence object? at
/usr/lib/perl5/site_perl/5.8.5/Bio/Perl.pm line 283
        Bio::Perl::write_sequence('>roa1.fasta', 'fasta', 'undef') called at
bt1.pl line 10


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