[Bioperl-l] bioperl 1.4 SearchIO doesn't work parsing blast output
Pieter Monsieurs
Pieter.Monsieurs at esat.kuleuven.be
Fri Feb 10 09:44:10 UTC 2006
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
>
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