[Bioperl-l] blast_sequence problem

Regina Schmitt rschmit6 at jhmi.edu
Tue Apr 13 12:07:16 EDT 2004


   Thanks for your reply. I installed Perl 5.8.0 and for whatever 
reason, that works fine. I ran the code with the debugger but wasn't 
able to figure out the problem. But it works with new version and that's 
good enough for me! Thanks again.


Barry Moore wrote:

> Regina,
> Your question is appropriate for the list.  I can't recreate that 
> error message.  That script works fine for me on XP (but I'm using 
> Perl 5.8.0).  Try running it with the Perl debugger ( perl -d 
> yourscript.pl)  and use "s" to step into the bioperl code and see if 
> you can pin down where that error is coming from.  Let us know how it 
> goes.
> Barry
> Regina Schmitt wrote:
>> Hello, my name is Regina and I'm new to the list. I've just installed 
>> Bioperl on Win XP and once I got around some problem with IO:String 
>> it seems to work fine. I am having a problem running the following 
>> script (from the tutorial) though:
>> $seq_object = get_sequence('swissprot',"ROA1_HUMAN");
>> $blast_result = blast_sequence($seq_object);
>> write_blast(">roa1.blast",$blast_result);
>> I get the following output:
>> Submitted Blast for [ROA1_HUMAN] --------------------WARNING 
>> --------------------- MSG:
>> --------------------------------------------------- .
>> and the output file is blank.
>> Since the warning message is blank, its kind of hard to
>> figure out whats wrong! I did a bunch of google searches
>> and came up with nothing. I also tried it with different sequence 
>> inputs.
>> I hope this is not a RTFM question and I am sorry if it is. I'm just 
>> wondering if there is some known bug or
>> perhaps it is something obviously wrong...its hard to tell. I know of 
>> other (newbies) who are having the same
>> problem. I am running Perl v5.6.1 btw. Thanks in advance for any ideas.
>> ~Regina
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>> Bioperl-l at portal.open-bio.org
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