[Bioperl-l] Array Handling Differences between RemoteBlast and StandAloneBlast

[Dave Messina]

Hi John,

You're right that passing parameters should work similarly for both RemoteBlast and StandAloneBlast, but without seeing exactly the parameter array you're passing, it's not possible to identify the problem.

Could you perhaps post a small, but complete test program that demonstrates the problem?


Dave


PS — is this the actual code you ran?

> My $Stand_alone_blast_machine=Tools::Run::StandAloneBlast(@standslone_blast_params);
> My $blast_report=$Stand_alone_blast_machine(@primer_info{primer});
> While (my $result=$blast_report->next_result()){
> [etc, etc for iteration]
> }

I'm guessing you were paraphrasing, but I ask because My, with a capital "M", will generate an error, you're calling Tools::Run::StandAloneBlast instead of Bio::Tools::Run::StandAloneBlast, and there's no method call to new(), i.e. it should be:

	my $Stand_alone_blast_machine = Bio::Tools::Run::StandAloneBlast->new(@standalone_blast_params);