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

[Ma, Man Chun John]

Hi,

I use bioperl-live 16950 with blast 2.2.23 I haven't been able to put
together a simplier script with problem at this time, so I'd put the
BLASTn outputs (in blast, blasttable and blastxml formats) here-- they
look perfectly normal except that look like 2 separate output files
appended together.

Cheers,


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: Saturday, May 08, 2010 4:47 PM
To: Ma, Man Chun John
Cc: BioPerl List
Subject: Re: [Bioperl-l] Array Handling Differences between RemoteBlast
and StandAloneBlast

There was a report last week of a possible problem with BLAST parsing
introduced in the last few days. I don't know what the status of that
is, but it's possible that it's related.

In any case, if you post your code and the blast report you're parsing,
we might be able to diagnose the problem. Also, what version of BioPerl
are you using?


Dave



On May 8, 2010, at 11:37 PM, Ma, Man Chun John wrote:

> Hi,
> 
> And that's my problem here: I checked the BLAST output, and the two 
> sequences did get aligned-- just that SearchIO, in whatever flavour (I

> tried blast, blasttable and blastxml) didn't see to do to the next 
> result when next_result() is called. It knows there're two results, 
> but still getting the first result  on the second call.
> 
> Cheers,
> 
> 
> 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: Saturday, May 08, 2010 4:33 PM
> To: Ma, Man Chun John
> Cc: BioPerl List
> Subject: Re: [Bioperl-l] Array Handling Differences between 
> RemoteBlast and StandAloneBlast
> 
> 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_b
>>> l
>>> a
>>> 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);
>> 
>> 
>> 
>> __________ Information from ESET NOD32 Antivirus, version of virus 
>> signature database 5095 (20100507) __________
>> 
>> The message was checked by ESET NOD32 Antivirus.
>> 
>> http://www.eset.com
>> 
> 

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