[Bioperl-l] RemoteBlast.pm getting RID requests-make/alter the method?

Roger Hall roger at iosea.com
Mon Feb 6 13:14:11 EST 2006


I decided to fix this module about ten days ago, and then was out all of
last week with Strep plus a virus or two - it's one of the advantages of
having young kids.

I see that there have been quite a few messages about this module in just
the last week. I am sitting down now to read through them.

I'll get back to you (and the list) ASAP.

If you have any other questions or suggestions about RemoteBlast, feel free
to bug me with 'em. 

Roger Hall
Technical Director
MidSouth Bioinformatics Center
University of Arkansas at Little Rock

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Bradley J. S. C.
Sent: Friday, February 03, 2006 2:54 PM
To: bioperl-l at lists.open-bio.org
Subject: [Bioperl-l] RemoteBlast.pm getting RID requests-make/alter the

I have been working with the RemoteBlast.pm module and have found that it is
a bit clunky to use loops to keep checking to see if you RID has finished.


For example, every time you write a script, you need to add a code block
(see example in the documentation) in order to keep checking if @rid is


Would it be better to maybe write this in as a method in the RemoteBlast
module?  It seems like it would be better for remoteblast to have a method
we could call say retrieve_when_done that would return the blast report when
the value of retrieve_blast is no longer 0.


The only issue may be report parsing, but I wonder if it might be better to
separate out submittal/retrieval of BLAST requests from the parsing step and
make these more discrete processes?  Since NCBI seems to be not supporting
text results as a standard, maybe the module should work exclusively with
XML and we could change report handling away from the headaches of text
processing and just allow Bio::SeqIO or blastxml handle the task of making a
blast reports into different forms (such as HTML, text etc).


This would definitely simplifying coding using the RemoteBlast.pm module as
then you could treat the report retrieval process as an object and just wait
for the object to return its value, instead of coding in a bunch of test
loops to see if it is done.  This may also help keep bugs out of the module
and make the module longer lasting and not require module users to rewrite
their code every time NCBI makes changes.


Any thoughts or ideas?


Is anyone working on this?




Brad Olson



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