[Bioperl-l] BLAST Parsing Bug?

Tue, 20 Aug 2002 12:55:22 -0400 (EDT)

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]
> >
> >
> >
> >
> > _______________________________________________
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> 
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 