[Bioperl-l] Strangeness in parsing blast file

[Sendu Bala]

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?

>    `$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())?

Btw, 
http://perldoc.perl.org/perlfaq8.html#What's-wrong-with-using-backticks-in-a-void-context%3f


> 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().