[Bioperl-l] BLAST Parsing Bug?

[Paul Boutros]

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]