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

[Dave Messina]

Hi John,

Please remember to keep Cc'ing the mailing list so that everyone can participate in the discussion.

If I understand your question correctly, yes, you can iterate through the blast results in a report called $blast_report using next_result.

If you haven't already, you may want to look at the SearchIO HOWTO:

http://www.bioperl.org/wiki/HOWTO:SearchIO

(although the BioPerl website appears to be temporarily offline, so check back a little later.)


Dave



On May 8, 2010, at 11:16 PM, Ma, Man Chun John wrote:

> Hi,
> 
> I have did some more investigation and found that the issue is probably
> that of SearchIO rather than StandAloneBlast--in case I made a mistake,
> so if I parsed a standard @array of Bio::Seq objects into
> StandAloneBlast (blastn with SearchIO output), the result for each of
> the seqs in the array can be assessed by $blast_report->next_result,
> right?
> 
> 
> John MC Ma
> Graduate Assistant
> Kwitek Lab
> Department of Internal Medicine
> 3125E MERF
> 375 Newton Road
> Iowa City IA 52242
> -----Original Message-----
> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
> Sent: Friday, May 07, 2010 5:34 PM
> To: Ma, Man Chun John
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Array Handling Differences between RemoteBlast
> and StandAloneBlast
> 
> 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_bla
>> st_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);
> 
> 
> 
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