[Bioperl-l] BLASTing with a seqio/seq object...

Sendu Bala bix at sendu.me.uk
Mon Dec 4 09:37:16 EST 2006

Samantha Thompson wrote:
> Hi,
> Thanks for all your help so far, I am still trying to understand a 
> couple of things...

You should make sure your replies are sent to the list, as you're likely 
to get a faster response.

[where $blast_report is the value returned by 
> when I run this line..
> $searchio = Bio::SearchIO->new(-format <http://www.perldoc.com/perl5.6/pod/func/format.html> => 'blast',
>                                -file   => $blast_report);
> between submitting the blast search and trying to to process the searchio object like I was attempting before I get the following errors back:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Could not open 1: No such file or directory
> Does this mean that my BLAST is failing when I submit it?

No, the -file option of SearchIO->new() takes, unsurprisingly, a 
filename. I'd tell you to pay careful attention to the docs, but sadly 
the RemoteBlast docs are currently wrong.

submit_blast() claims to return 'Blast report object' (which in any case 
certainly wouldn't be a filename) when in fact it returns, as you 
discovered, a (for our purposes) meaningless number.

As I suggested before, you need to look at the synopsis for 
Bio::Tools::Run::RemoteBlast instead.

(having called submit_blast you must do the each_rid loop)

Does anyone care to go through the POD for RemoteBlast and update it to 
an accurate state?

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