[Bioperl-l] bioperl 1.4 SearchIO doesn't work parsing blast output
Roger Hall
rahall2 at ualr.edu
Fri Feb 10 18:00:51 UTC 2006
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
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>>>>>>>>--
>>>>>>>>Jason Stajich
>>>>>>>>Duke University
>>>>>>>>http://www.duke.edu/~jes12
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>Christopher Fields
>>>>>>>Postdoctoral Researcher - Switzer Lab
>>>>>>>Dept. of Biochemistry
>>>>>>>University of Illinois Urbana-Champaign
>>>>>>>
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>>>>>
>>>>>
>>>>>
>>>>>
>>>Christopher Fields
>>>Postdoctoral Researcher
>>>Lab of Dr. Robert Switzer
>>>Dept of Biochemistry
>>>University of Illinois Urbana-Champaign
>>>
>>>
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>>>
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