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

Chris Fields cjfields at uiuc.edu
Fri Feb 10 13:08:37 EST 2006


Makes sense.  I didn't see this since I passed the files directly from
command-line.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign  

> -----Original Message-----
> From: Roger Hall [mailto:rahall2 at ualr.edu] 
> Sent: Friday, February 10, 2006 12:01 PM
> To: 'Hubert Prielinger'; 'Pieter Monsieurs'; 
> bioperl-l at bioperl.org; 'Chris Fields'
> Subject: RE: [Bioperl-l] bioperl 1.4 SearchIO doesn't work 
> parsing blast output
> 
> Hubert,
> 
> I got the same message when I first ran your script. The 
> issue for me was that "readdir(DIR)" doesn't return the full 
> path, only the file name.
> 
> I edited your script to include:
> 
> 	$file = $directory . '/' . $file;
> 
> just before the Bio::SearchIO call.
> 
> Roger
> 
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Hubert Prielinger
> Sent: Friday, February 10, 2006 10:27 AM
> To: Pieter Monsieurs; bioperl-l at bioperl.org; Chris Fields; 
> rahall2 at ualr.edu
> Subject: Re: [Bioperl-l] bioperl 1.4 SearchIO doesn't work 
> parsing blast output
> 
> Hi,
> I'm sorry for disturbing once more. Yesterday the script was 
> working, today it isn't working at all, but I didn't change 
> anything, I get the following error message:
> 
> ------------- EXCEPTION  -------------
> MSG: Could not open comp80swiss2114.txt: No such file or 
> directory STACK Bio::Root::IO::_initialize_io
> /usr/lib/perl5/site_perl/5.8.6/Bio/Root/IO.pm:273
> STACK Bio::Root::IO::new 
> /usr/lib/perl5/site_perl/5.8.6/Bio/Root/IO.pm:213
> STACK Bio::SearchIO::new 
> /usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO.pm:135
> STACK Bio::SearchIO::new 
> /usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO.pm:167
> STACK toplevel ./Blast.pl:14
> 
> --------------------------------------
> 
> the file exists and the bug I have fixed yesterday thanks for help
> 
> Hubert
> 
> 
> 
> 
> Pieter Monsieurs wrote:
> 
> > Sorry for disturbing. I now works correctly with the bug 
> fix of Chris. 
> > Thanx,
> > Pieter
> >
> > Pieter Monsieurs wrote:
> >
> >>Hi Chris,
> >>
> >>The parsing of the Blast output still doesn't work for me 
> with the bug 
> >>fix download of blast.pm.
> >>The module keeps turning around in the while loop at line 
> 487 looking 
> >>for a database or query-size:
> >>
> >>while( defined ($_) ) {
> >>	if( /^Database:/ ) {
> >>		$self->_pushback($_);
> >>		last;
> >>	}
> >>	chomp;               
> >>	if( /\((\-?[\d,]+)\s+letters.*\)/ || /^Length=(\-?[\d,]+)/ ) {
> >>		$size = $1;
> >>		$size =~ s/,//g;
> >>		last;
> >>	} else {
> >>		$q .= " $_";
> >>		$q =~ s/ +/ /g;
> >>		$q =~ s/^ | $//g;
> >>	}
> >>	$_ = $self->_readline;
> >>}
> >>
> >>
> >>The code keeps looking for the database information, 
> however - as you 
> >>mentioned - this information is given before the query line 
> in the new 
> >>Blast output format.
> >>This way, all hits and hsps are stored in the query_description 
> >>($hit->query_description), no hits are found and query_length is 0.
> >>Because you already adapted the module to retrieve database 
> >>information at another position in the module, deleting the 
> while loop 
> >>and adding the following lines after $_ = $self->_readline 
> (line 486), 
> >>worked fine for me (using blastn and blastp):
> >>
> >>if (/Length=([\d,]+)/) {
> >>	$size = $1;
> >>	$size =~ s/,//g;
> >>}
> >>
> >>
> >>Regards,
> >>Pieter
> >>
> >>
> >>
> >>Chris Fields wrote:
> >>
> >>  
> >>
> >>>From 'perldoc Bio::SearchIO::blast':
> >>>
> >>>DESCRIPTION
> >>>       This object encapsulated the necessary methods for 
> generating 
> >>>events
> >>>       suitable for building Bio::Search objects from a 
> BLAST report 
> >>>file.
> >>>       Read the Bio::SearchIO for more information about 
> how to use 
> >>>this.
> >>>
> >>>       This driver can parse:
> >>>
> >>>       o   NCBI produced plain text BLAST reports from blastall,  
> >>>this also
> >>>           includes PSIBLAST, PSITBLASTN, RPSBLAST, and bl2seq 
> >>>reports.  NCBI
> >>>           XML BLAST output is parsed with the blastxml SearchIO 
> >>>driver
> >>>
> >>>       o   WU-BLAST all reports
> >>>
> >>>       o   Jim Kent's BLAST-like output from his programs 
> (BLASTZ,  
> >>>BLAT)
> >>>
> >>>       o   BLAST-like output from Paracel BTK output
> >>>
> >>>So, it should.  Let us know if it doesn't.
> >>>
> >>>On Feb 9, 2006, at 4:20 PM, Hubert Prielinger wrote:
> >>>
> >>> 
> >>>
> >>>    
> >>>
> >>>>Hi Chris,
> >>>>I'm incredibly sorry for causing so much inconvenience, 
> yes you are 
> >>>>right, I had only to change the blast.pm file, it is working very 
> >>>>fine, thank you very much, and you are right, you have 
> mentioned it 
> >>>>ealier either to change the file... ;)
> >>>>
> >>>>but I have another question: does it work with the 
> WU-Blast output 
> >>>>too?
> >>>>regards
> >>>>Hubert
> >>>>
> >>>>
> >>>>Chris Fields wrote:
> >>>>
> >>>>   
> >>>>
> >>>>      
> >>>>
> >>>>>Ha!  I come back from meeting and there's a billion 
> emails!  What 
> >>>>>have we started? ;p .  Sorry about this Jason; I know 
> you're busy.
> >>>>>
> >>>>>Hubert, if you're out there, I sent you an email with an 
> >>>>>attachment.  You said the output looks like what you were 
> >>>>>expecting.  So I think we have two
> >>>>>problems:
> >>>>>
> >>>>>1)  I haven't delved into the file scanning, but the 
> fact that it 
> >>>>>takes so long should tell you something's seriously 
> wrong there.  
> >>>>>Strip that part out and start with a simple script, say, 
> like the 
> >>>>>one Jason or that I sent you; the script I used to generate that 
> >>>>>output works fine (on two OS's, WinXP and Mac OS X).  
> Use it on one 
> >>>>>file at a time.  Do everything on command line (not through 
> >>>>>Eclipse).  IDE's can be notoriously flaky about running scripts, 
> >>>>>esp. when they run debugging.
> >>>>>2) Even if you have bioperl-1.5.1 installed, 
> Bio::SearchIO::blast 
> >>>>>will still not work whenever the text blast output has the 
> >>>>>following header, which comes from the new web version of BLAST:
> >>>>>
> >>>>>-----------------------------------------------------
> >>>>>BLASTP 2.2.13 [Nov-27-2005]
> >>>>>Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A.  
> >>>>>Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and 
> David J.  
> >>>>>Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of 
> >>>>>protein database search programs", Nucleic Acids Res. 
> 25:3389-3402.
> >>>>>
> >>>>>RID: 1139501210-857-165793005128.BLASTQ1
> >>>>>
> >>>>>
> >>>>>Database: All non-redundant GenBank CDS
> >>>>>translations+PDB+SwissProt+PIR+PRF excluding 
> environmental samples
> >>>>>         3,292,813 sequences; 1,128,164,434 total 
> letters Query=  
> >>>>>NP_215895 pyrimidine regulatory protein PyrR [Mycobacterium 
> >>>>>tuberculosis H37Rv].
> >>>>>Length=193
> >>>>>.......
> >>>>>-----------------------------------------------------
> >>>>>
> >>>>>It will work if the text output has the following header 
> (or is an 
> >>>>>older version of BLAST):
> >>>>>
> >>>>>-----------------------------------------------------
> >>>>>BLASTP 2.2.12 [Aug-07-2005]
> >>>>>
> >>>>>
> >>>>>Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A.  
> >>>>>Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.  
> >>>>>Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of 
> >>>>>protein database search programs",  Nucleic Acids Res. 
> >>>>>25:3389-3402.
> >>>>>
> >>>>>Query= NP_215895 pyrimidine regulatory protein PyrR 
> [Mycobacterium 
> >>>>>tuberculosis H37Rv].
> >>>>>       (193 letters)
> >>>>>
> >>>>>Database: All non-redundant GenBank CDS
> >>>>>translations+PDB+SwissProt+PIR+PRF excluding 
> environmental samples
> >>>>>         2,895,325 sequences; 997,103,285 total letters
> >>>>>-----------------------------------------------------
> >>>>>You have the former (2.2.13) version.  I know b/c I have 
> your BLAST 
> >>>>>files.
> >>>>>Therefore, even bioperl-1.5.1 will not work!
> >>>>>
> >>>>>If you want the really gory details on why this is a 
> problem, look
> >>>>>here:
> >>>>>
> >>>>>http://bugzilla.bioperl.org/show_bug.cgi?id=1934
> >>>>>
> >>>>>So, any text output with the above header will not work; it will 
> >>>>>either hang or end abruptly (depending on OS, perl 
> version, memory, 
> >>>>>patience).  If you look in the above, I have added a preliminary 
> >>>>>fix for this.  I'll reiterate for the billionth time, it hasn't 
> >>>>>been committed yet, so don't kill me if blows your 
> computer up ;> 
> >>>>>Here's the direct link:
> >>>>>http://bugzilla.bioperl.org/attachment.cgi?id=267&action=view
> >>>>>This is a modified version of Bio::SearchIO::blast.pm 
> (it says it's 
> >>>>>version 1.90, but it's lying, I didn't change the 
> version, only the 
> >>>>>regex; sorry Jason).  From what you've been posting it doesn't 
> >>>>>sound like you've tried this, and I believe I've 
> suggested this fix 
> >>>>>before.
> >>>>>
> >>>>>Replace the one in your Bio/SearchIO directory (which looks like 
> >>>>>'/usr/lib/perl5/site_perl/5.8.6/Bio/SearchIO/', judging 
> from your 
> >>>>>prev.
> >>>>>message) with this file.  Make sure the filename stays the same 
> >>>>>(blast.pm).
> >>>>>
> >>>>>Run everything again, one file at a time.  Make sure you use 
> >>>>>Jason's script as well as the one I sent you.  Do NOT rely on 
> >>>>>running through multiple files yet.  Fix one bug at a time.  And 
> >>>>>heed Joel's words about file checks.
> >>>>>
> >>>>>
> >>>>>Here's a small chunk of output from one of your blast 
> files using 
> >>>>>the modifed script I sent you:
> >>>>>
> >>>>>sp|Q10264|PSO2_SCHPO-->DNA cross-link repair protein pso2/snm1
> >>>>>Query:   1  RWKWKRKK  8
> >>>>>Seq:     542  RWAWRRKK  549
> >>>>>
> >>>>>Look familiar?
> >>>>>
> >>>>>Christopher Fields
> >>>>>Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry 
> >>>>>University of Illinois Urbana-Champaign
> >>>>>
> >>>>>     
> >>>>>
> >>>>>        
> >>>>>
> >>>>>>-----Original Message-----
> >>>>>>From: Roger Hall [mailto:rahall2 at ualr.edu] Sent: Thursday, 
> >>>>>>February 09, 2006 3:24 PM
> >>>>>>To: 'Hubert Prielinger'; 'Chris Fields'; 'Jason Stajich'
> >>>>>>Subject: RE: [Bioperl-l] bioperl 1.4 SearchIO doesn't 
> work parsing 
> >>>>>>Blast output
> >>>>>>
> >>>>>>In other words, yes, I'm on the wrong trail. :}
> >>>>>>
> >>>>>>Sorry - I'll look at the output issue this evening (or realize 
> >>>>>>that Chris already solved the issue).  ;}
> >>>>>>
> >>>>>>Thanks!
> >>>>>>
> >>>>>>Roger
> >>>>>>
> >>>>>>-----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: Thursday, February 09, 2006 2:14 PM
> >>>>>>To: rahall2 at ualr.edu; bioperl-l at bioperl.org; Chris 
> Fields; Jason 
> >>>>>>Stajich
> >>>>>>Subject: Re: [Bioperl-l] bioperl 1.4 SearchIO doesn't 
> work parsing 
> >>>>>>Blast output
> >>>>>>
> >>>>>>dear roger,
> >>>>>>this error message I got, when I tried to parse Blast output 
> >>>>>>(version
> >>>>>>2.2.12) with bioperl 1.5.1, but it doesn't matter, 
> because I have 
> >>>>>>a lot of Blast output files with version 2.2.13 and for that I 
> >>>>>>don't get any error message.....it just doesn't work
> >>>>>>
> >>>>>>Hubert
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>Roger Hall wrote:
> >>>>>>
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>Guys - I'm looking at the 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
> >>>>>>>
> >>>>>>>This is my line of thought:
> >>>>>>>1. "no data for midline $_" is a unique message generated by
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>blast.pm
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>in
> >>>>>>>
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>one
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>location only at the point of a. reading three lines b.
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>dropping lines
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>with spaces only c. identifying the Query, Midline, and
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>Match lines (0
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>><= $i <
> >>>>>>>
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>3)
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>2. There is a regexp match that fails in order to reach that
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>error message
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>3. The $_ value "Query  1   WWWKWRW  7" should not fail the
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>expression
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>4. It does anyway
> >>>>>>>5. I cannot find the value "Query  1   WWWKWRW  7" anywhere
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>in the blast
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>reports
> >>>>>>>
> >>>>>>>I suspect a newline/chomp/metacharacter issue. Not finding
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>the string
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>anywhere has me thoroughly confused - I asked Hubert for the
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>additional
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>file, assuming that I didn't have it.
> >>>>>>>
> >>>>>>>My next thought is to write a quick script to test 
> perl behavior 
> >>>>>>>on "Fedora Core 9".
> >>>>>>>
> >>>>>>>Thoughts?
> >>>>>>>
> >>>>>>>Did I misread the issue entirely? :}
> >>>>>>>
> >>>>>>>Roger
> >>>>>>>
> >>>>>>>
> >>>>>>>-----Original Message-----
> >>>>>>>From: bioperl-l-bounces at lists.open-bio.org
> >>>>>>>[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>Chris Fields
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>Sent: Thursday, February 09, 2006 10:16 AM
> >>>>>>>To: 'Jason Stajich'; 'Hubert Prielinger'
> >>>>>>>Cc: bioperl-l at bioperl.org
> >>>>>>>Subject: Re: [Bioperl-l] bioperl 1.4 SearchIO doesn't work 
> >>>>>>>parsing Blast output
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>>>-----Original Message-----
> >>>>>>>>From: Jason Stajich [mailto:jason.stajich at duke.edu]
> >>>>>>>>Sent: Thursday, February 09, 2006 9:13 AM
> >>>>>>>>To: Hubert Prielinger
> >>>>>>>>Cc: Chris Fields; bioperl-l at bioperl.org
> >>>>>>>>Subject: Re: [Bioperl-l] bioperl 1.4 SearchIO doesn't work 
> >>>>>>>>parsing Blast output
> >>>>>>>>
> >>>>>>>>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";	
> >>>>>>>>>
> >>>>>>>>>             
> >>>>>>>>>
> >>>>>>>>>                
> >>>>>>>>>
> >>>>>>>>     }
> >>>>>>>> }
> >>>>>>>>}
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>           
> >>>>>>>>
> >>>>>>>>              
> >>>>>>>>
> >>>>>>>I tested some of the BLAST results that Hubert sent Roger
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>and me with a
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>similar script to the above.  I removed the file parsing logic 
> >>>>>>>and it
> >>>>>>>
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>seemed
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>to work just fine.  It may very well be a logic issue or
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>that he hasn't
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>installed the latest fix.
> >>>>>>> It's a funny thing, though.  When I tried using blastcl3 (v.
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>2.2.13),
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>even though the returned output was from nr, the top 
> of the blast 
> >>>>>>>output showed that it was v2.2.12:
> >>>>>>>
> >>>>>>>BLASTP 2.2.12 [Aug-07-2005]
> >>>>>>>
> >>>>>>>I double-checked my local version and it's definitely v.2.2.13:
> >>>>>>>-------------------------------------
> >>>>>>>C:\Perl\Scripts>blastcl3 -
> >>>>>>>
> >>>>>>>blastcl3 2.2.13   arguments:...
> >>>>>>>-------------------------------------
> >>>>>>>
> >>>>>>>If you use RemoteBlast using the same settings, the version in 
> >>>>>>>the header looks like this:
> >>>>>>>
> >>>>>>>BLASTP 2.2.13 [Nov-27-2005]
> >>>>>>>
> >>>>>>>I'm wondering if all the blast executables (blast and netblast)
> >>>>>>>            
> >>>>>>>
> >>>>>>>from NCBI have text output like v.2.2.12, while the wwwblast
> >>>>>>          
> >>>>>>
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>outputs a new
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>format (2.2.13).  I'll ask blast-help at NCBI about this.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>>>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.
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>           
> >>>>>>>>
> >>>>>>>>              
> >>>>>>>>
> >>>>>>>Does XML lack some specific info that text output has?
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>Didn't know that.
> >>>>>>I
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>>>believe that XML should be default in RemoteBlast 
> since it will 
> >>>>>>>not break, but I agree with you about text output.  I 
> also agree 
> >>>>>>>that it will need somebody to maintain it constantly, 
> much like 
> >>>>>>>RemoteBlast.
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>>>-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
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>
> >>>>>>>>>>>                 
> >>>>>>>>>>>
> >>>>>>>>>>>                    
> >>>>>>>>>>>
> >>>>>>>>>>               
> >>>>>>>>>>
> >>>>>>>>>>                  
> >>>>>>>>>>
> >>>>>>>>>_______________________________________________
> >>>>>>>>>Bioperl-l mailing list
> >>>>>>>>>Bioperl-l at lists.open-bio.org
> >>>>>>>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>             
> >>>>>>>>>
> >>>>>>>>>                
> >>>>>>>>>
> >>>>>>>>--
> >>>>>>>>Jason Stajich
> >>>>>>>>Duke University
> >>>>>>>>http://www.duke.edu/~jes12
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>
> >>>>>>>>           
> >>>>>>>>
> >>>>>>>>              
> >>>>>>>>
> >>>>>>>Christopher Fields
> >>>>>>>Postdoctoral Researcher - Switzer Lab Dept. of Biochemistry 
> >>>>>>>University of Illinois Urbana-Champaign
> >>>>>>>
> >>>>>>>_______________________________________________
> >>>>>>>Bioperl-l mailing list
> >>>>>>>Bioperl-l at lists.open-bio.org
> >>>>>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>         
> >>>>>>>
> >>>>>>>            
> >>>>>>>
> >>>>>>_______________________________________________
> >>>>>>Bioperl-l mailing list
> >>>>>>Bioperl-l at lists.open-bio.org
> >>>>>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>>>>
> >>>>>>
> >>>>>>       
> >>>>>>
> >>>>>>          
> >>>>>>
> >>>>>     
> >>>>>
> >>>>>        
> >>>>>
> >>>Christopher Fields
> >>>Postdoctoral Researcher
> >>>Lab of Dr. Robert Switzer
> >>>Dept of Biochemistry
> >>>University of Illinois Urbana-Champaign
> >>>
> >>>
> >>>
> >>>
> >>>_______________________________________________
> >>>Bioperl-l mailing list
> >>>Bioperl-l at lists.open-bio.org
> >>>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>>
> >>> 
> >>>
> >>>    
> >>>
> >>
> >>
> >>Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm
> >>
> >>_______________________________________________
> >>Bioperl-l mailing list
> >>Bioperl-l at lists.open-bio.org
> >>http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>  
> >>
> >
> >
> > Disclaimer: 
> http://www.kuleuven.be/cwis/email_disclaimer.htm for more 
> > information.
> >
> 
> _______________________________________________
> Bioperl-l mailing list
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