[Bioperl-l] Strangeness in parsing blast file

[Chris Fields]

As an aside, BLAST 2.2.13 or later cannot be parsed using Bioperl  
1.5.1.  You have to update to the latest bioperl-live (from CVS).

Chris

On Jul 30, 2006, at 7:13 PM, Nabil Hafez wrote:

>
>
> Sendu Bala wrote:
>
>> Nabil Hafez wrote:
>>
>>
>>> I had modified the variables a bit to try and make them more  
>>> readable
>>> than what is in my code, in my code -o $blastoutput is
>>> what it is, like I said, the blast portion works absolutely fine  
>>> - i.e.
>>> the do_blast sub routine is fully functional.
>>>
>>>
>>
>> How do you know?
>>
>>
>>
> Because it creates a file containing all of the blastoutput, this  
> works
> every time - a file is created with the
> blastoutput.
>
>>>   `$MBLAST -d $blastdb -e $e_val -p $percent_id -D 2 -i $bf -o
>>> $blastoutput`;
>>>
>>>
>>
>> Does this command definitely produce exactly the same file as the one
>> you use to show that parse_blast() does sometimes work (when you  
>> avoid
>> using do_blast())?
>>
>>
>>
> Yes - the exact same file because I produce the file with  do_blast()
> and then when it fails to parse it ends but
> there is a blastoutput file created in my directory.  If i re-run the
> script again just feeding in the name of the file that was
> created, it parses it just fine.  So basically the parsing works
> whenever I feed it a blastoupt file but it can't seem to parse
> the same file that was created and then passed to the  parse_blast()
> subroutine
>
>> Btw,
>> http://perldoc.perl.org/perlfaq8.html#What's-wrong-with-using- 
>> backticks-in-a-void-context%3f
>>
>> Good to know. Thanks.
>>
>>
>>> I will try your suggestion to use the  
>>> Bio::Tools::Run::StandaloneBlast,
>>> is megablast supported by this module?
>>>
>>>
>>
>> No, it doesn't. You could cheat and call _runblast() directly  
>> (give it
>> an executable string and a string of args to megablast), and provide
>> -outfile to new().
>>
>>
>>
> I still don't think the blast is a problem since I get perfect
> blastoutput everytime.
>
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>>
>>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign