[Bioperl-l] BLAST Parsing Bug?
Andreas Matern
andreas.matern@lbri.lionbioscience.com
Tue, 20 Aug 2002 12:39:26 -0400
This code works fine for me using Win2k
I didn't do the activestate perl build, however, perhaps that is bugged.
I just downloaded the bioperl 1.0.2 tarball and uncompressed in into
C:\Perl\site\lib
I normally don't use Win2k however, I generaly use the CVS version of
bioperl which tends to work fine...
And bioperl is EXTREMELY useful for me, great job bioperlers....
-Andreas
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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--
--------------
Andreas Matern
Bioinformatician
Bioinformatics - Research and Development
Lion Bioscience Research Inc.
141 Portland Street, 10th floor
Cambridge, MA 02139 USA
Phone: 617-245-5483
Fax: 617-245-5499
amatern@lbri.lionbioscience.com
www.lionbioscience.com