[Bioperl-l] blast_sequence problem

[Regina Schmitt]

Barry,

   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.

~Regina

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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>
>
>