[Bioperl-l] Strangeness in parsing blast file

[Nabil Hafez]

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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