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

Bradley J. S. C. Olson olsonbr2 at msu.edu
Fri Feb 3 15:54:22 EST 2006

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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