[Bioperl-l] BLAST Parsing Bug?

Jason Stajich jason@cgt.mc.duke.edu
Tue, 20 Aug 2002 13:25:21 -0400 (EDT)


I'm pretty sure even if you tell blastall that you don't want to see any
alignments (-b 0) you still get them when you ask for -m7 output.


On Tue, 20 Aug 2002, Paul Boutros wrote:

> Is this true for the blastxml parser as well?
>
> On Tue, 20 Aug 2002, Jason Stajich wrote:
>
> > Because the parser expects to be parsing a full blast report - you are
> > only providing it with a report which has hits but no hsps.
> >
> > At some point we can adapt the module to parse these types of reports, but
> > for now it is only going to work with reports that have the full
> > alignments included.
> >
> > -jason
> >
> > On Tue, 20 Aug 2002, Paul Boutros wrote:
> >
> > > Hello,
> > >
> > > I am just starting with Bioperl, trying to evaluate how useful it will be
> > > for our group.  I'm struggling with getting it to work on my first few
> > > steps here, though.  I would like to use the SearchIO system to parse a
> > > blast-results file and I can strange results.
> > >
> > > System: Win2k Pro (sp3)
> > > Perl: 5.6.1 ActiveState build 631 (all packages are updated)
> > > BioPerl: 1.00.2
> > >
> > > The basic problem is that the parser isn't finding any of the hits.  At
> > > all.  So the code below comes back with $count=0 for every record in the
> > > BLAST output file.  Any ideas what I'm doing wrong?
> > >
> > > Paul
> > >
> > >
> > > Code:
> > > use strict;
> > > use Bio::SearchIO;
> > >
> > > my $searchio = new Bio::SearchIO(
> > > 			'-format'	=> 'blast',
> > > 			'-file'		=> '15k5prime.out',
> > > 			);
> > >
> > > while (my $result = $searchio->next_result()) {
> > >
> > > 	my $count = 0;
> > >
> > > 	print "Name: ", $result->query_name(), "\n";
> > >
> > > 	while (my $hit = $result->next_hit()) {
> > > 		$count++;
> > > 		}
> > >
> > > 	print "Count: $count\n";
> > >
> > > 	}
> > >
> > > Blast File Fragment:
> > >
> > > BLASTN 2.2.3 [Apr-24-2002]
> > >
> > >
> > > 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= H3001A01-5
> > >          (589 letters)
> > >
> > > Database: est_others
> > >            5,032,538 sequences; 2,449,699,975 total letters
> > >
> > >
> > >
> > >                                                                  Score
> > > E
> > > Sequences producing significant alignments:                      (bits)
> > > Value
> > >
> > > gb|BQ206993.1|BQ206993 UI-R-DZ1-cnm-h-16-0-UI.s1 UI-R-DZ1 Rattus...   200
> > > 3e-050
> > > gb|BM386877.1|BM386877 UI-R-CN1-cjh-d-20-0-UI.s1 UI-R-CN1 Rattus...   198
> > > 1e-049
> > > gb|BI301905.1|BI301905 UI-R-DL0-cio-k-03-0-UI.s1 UI-R-DL0 Rattus...   198
> > > 1e-049
> > > gb|BI301460.1|BI301460 UI-R-DN0-cit-e-07-0-UI.s1 UI-R-DN0 Rattus...   198
> > > 1e-049
> > > gb|BG371847.1|BG371847 UI-R-CV0-brj-a-09-0-UI.s1 UI-R-CV0 Rattus...   198
> > > 1e-049
> > > gb|BE115424.1|BE115424 UI-R-BS1-axu-f-02-0-UI.s1 UI-R-BS1 Rattus...   198
> > > 1e-049
> > > gb|AA819696.1|AA819696 UI-R-A0-bh-d-10-0-UI.s1 UI-R-A0 Rattus no...   192
> > > 6e-048
> > > gb|BM383271.1|BM383271 UI-R-DS0-cje-i-16-0-UI.s1 UI-R-DS0 Rattus...   190
> > > 2e-047
> > > gb|BI292210.1|BI292210 UI-R-DN0-civ-m-09-0-UI.s1 UI-R-DN0 Rattus...   190
> > > 2e-047
> > > gb|BI284655.1|BI284655 UI-R-DE0-cac-f-05-0-UI.s1 UI-R-DE0 Rattus...   190
> > > 2e-047
> > >
> > >   Subset of the database(s) listed below
> > >      Number of letters searched: 123,827,604
> > >      Number of sequences searched:  285,629
> > >
> > >   Database: est_others
> > >     Posted date:  Aug 15, 2002 12:08 PM
> > >   Number of letters in database: 333,332,922
> > >   Number of sequences in database:  0
> > >
> > >   Database: c:\docume~1\paul\blast\data\est_others.01
> > >     Posted date:  Aug 15, 2002 12:21 PM
> > >   Number of letters in database: 333,333,126
> > >   Number of sequences in database:  734,123
> > >
> > >   Database: c:\docume~1\paul\blast\data\est_others.02
> > >     Posted date:  Aug 15, 2002 12:33 PM
> > >   Number of letters in database: 333,332,951
> > >   Number of sequences in database:  710,185
> > >
> > >   Database: c:\docume~1\paul\blast\data\est_others.03
> > >     Posted date:  Aug 15, 2002 12:45 PM
> > >   Number of letters in database: 333,332,998
> > >   Number of sequences in database:  651,575
> > >
> > >   Database: c:\docume~1\paul\blast\data\est_others.04
> > >     Posted date:  Aug 15, 2002 12:56 PM
> > >   Number of letters in database: 333,332,826
> > >   Number of sequences in database:  637,159
> > >
> > >   Database: c:\docume~1\paul\blast\data\est_others.05
> > >     Posted date:  Aug 15, 2002  1:07 PM
> > >   Number of letters in database: 333,333,104
> > >   Number of sequences in database:  630,795
> > >
> > >   Database: c:\docume~1\paul\blast\data\est_others.06
> > >     Posted date:  Aug 15, 2002  1:19 PM
> > >   Number of letters in database: 333,332,943
> > >   Number of sequences in database:  650,535
> > >
> > >   Database: c:\docume~1\paul\blast\data\est_others.07
> > >     Posted date:  Aug 15, 2002  1:28 PM
> > >   Number of letters in database: 116,369,105
> > >   Number of sequences in database:  227,351
> > >
> > > Lambda     K      H
> > >     1.37    0.711     1.31
> > >
> > > Gapped
> > > Lambda     K      H
> > >     1.37    0.711     1.31
> > >
> > >
> > > Matrix: blastn matrix:1 -3
> > > Gap Penalties: Existence: 5, Extension: 2
> > > Number of Hits to DB: 69,708
> > > Number of Sequences: 4241723
> > > Number of extensions: 69708
> > > Number of successful extensions: 25280
> > > Number of sequences better than  0.3: 2163
> > > length of query: 589
> > > length of database: 123,827,604
> > > effective HSP length: 18
> > > effective length of query: 571
> > > effective length of database: 118,686,282
> > > effective search space: 67769867022
> > > effective search space used: 67769867022
> > > T: 0
> > > A: 40
> > > X1: 6 (11.9 bits)
> > > X2: 15 (29.7 bits)
> > > S1: 12 (24.3 bits)
> > > S2: 19 (38.2 bits)
> > > BLASTN 2.2.3 [Apr-24-2002]
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> >
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu