[Bioperl-l] bioperl 1.4 SearchIO doesn't work parsing Blast output

[Jason Stajich]

On Feb 8, 2006, at 4:41 PM, Hubert Prielinger wrote:
> hi chris,
> thanks, I have upgraded to version 1.5.1 but it isn't still  
> working, do
> you have any ohter idea, the problem I have is that I have to parse a
> lot of textfiles....
> or shall I look for another option to parse those files...
>
> regards
> Hubert


The code from Bioperl 1.5.1 works fine for me for blast 2.2.13  
reports but unless you post your blast report we can't really  
determine the problem.

If you are still getting the same error like this I am not convinced  
you have upgraded to 1.5.1 which includes a fix in the fact that NCBI  
changed the HSP result format to remove the ':' from the Query/Sbjct  
prefixes.  We fixed this as soon as it was apparent sometime in  
September.

>>> MSG: no data for midline Query  1   WWWKWRW  7
>>> STACK Bio::SearchIO::blast::next_result
>>> /usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1151
>>> STACK toplevel
>>> /home/Hubert/installed/eclipse/workspace/Database_Search/Blast.pl:21

If you are just getting no results but also no warnings wrt parsing,  
are you sure your logic is correct?

If you remove your filters do you see all the HSPS?


while (my $result = $search->next_result) {
     print $result->query_name, "\n";
     #iterate over each hit on the query sequence
     while (my $hit = $result->next_hit) {
	print $hit->name, "\n";
         #iterate over each HSP in the hit
         while (my $hsp = $hit->next_hsp) {
	 print $hsp->evalue, " ", $hsp->length('sbjct'), " ", $hsp- 
 >hit_string, "\n";	
        }
    }
}


To clarify some stuff -
Chris I don't necessarily think the XML is best way forward for BLAST  
reports generated locally, it isn't as detailed as the Text format  
and it is what most people expect to be able to scroll through and  
parse -- it is also harder for the format to change dramatically if  
you have a static binary on your machine =).  I think for remoteblast  
the XML format should be the way forward but I expect Bioperl to  
maintain support of any plain text BLAST report format that people  
use on a regular basis.

-jason
>
>
> Chris Fields wrote:
>
>> My guess is you're running into text parsing problems in
>> Bio::SearchIO::blast.  Upgrade to the latest developer version  
>> (1.5.1) or
>> bioperl-live (CVS), then see the bug below.
>>
>> http://bugzilla.bioperl.org/show_bug.cgi?id=1934
>>
>> I think the first problem you ran into is solved in bioperl 1.5.1,  
>> the last
>> problem (more recent, not related to the first) has been fixed but  
>> hasn't
>> been committed to bioperl-live yet.  The fixed SearchIO::blast is  
>> available
>> in the link above, but realize it hasn't been committed yet and  
>> may change.
>>
>> Christopher Fields
>> Postdoctoral Researcher - Switzer Lab
>> Dept. of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>>> -----Original Message-----
>>> From: bioperl-l-bounces at lists.open-bio.org
>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>>> Hubert Prielinger
>>> Sent: Wednesday, February 08, 2006 2:52 PM
>>> To: bioperl-l at bioperl.org
>>> Subject: [Bioperl-l] bioperl 1.4 SearchIO doesn't work
>>> parsing Blast output
>>>
>>> Hi,
>>> If I want to parse a Blast Output (Version 2.2.12) with
>>> Bio::SearchIO, I get the following error message:
>>>
>>> MSG: no data for midline Query  1   WWWKWRW  7
>>> STACK Bio::SearchIO::blast::next_result
>>> /usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/blast.pm:1151
>>> STACK toplevel
>>> /home/Hubert/installed/eclipse/workspace/Database_Search/Blast.pl:21
>>>
>>> is that a bug......
>>>
>>> If I want to parse Blast Output (version 2.2.13), I don't get
>>> anything.....
>>> I'm using bioperl 1.4
>>>
>>> before, I have installed bioperl 1.4, it worked fine parsing
>>> Blast Output (version 2.2.12), but I don't remember which
>>> bioperl version I had installed
>>>
>>> thanks in advance
>>>
>>> Hubert
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
>>
>>
>>
>
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12