[Bioperl-l] BLASTing with a seqio/seq object...
bix at sendu.me.uk
Mon Dec 4 09:37:16 EST 2006
Samantha Thompson wrote:
> 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
(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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