Module Discussion:Bio::SearchIO::blastxml

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Using a recent SVN co of bioperl-live (revision 14980), I am trying to count the number of results with:

my $parser =
  new Bio::SearchIO( -format => 'blastxml',
		     -file   => 'my.blast.out.xml' );
 
warn "parsed (", $parser->result_count(), ")\n";

However, I get the following error:

------------- EXCEPTION: Bio::Root::NotImplemented -------------
MSG: Abstract method "Bio::SearchIO::result_count" is not implemented by package Bio::SearchIO::blastxml.
This is not your fault - author of Bio::SearchIO::blastxml should be blamed!

STACK: Error::throw
STACK: Bio::Root::Root::throw /homes/dbolser/perl5/lib/perl5/Bio/Root/Root.pm:357
STACK: Bio::Root::RootI::throw_not_implemented /homes/dbolser/perl5/lib/perl5/Bio/Root/RootI.pm:680
STACK: Bio::SearchIO::result_count /homes/dbolser/perl5/lib/perl5/Bio/SearchIO.pm:410
STACK: ./visualizeBlastHitsToChr.plx:34
----------------------------------------------------------------

This is annoying, because when I use the -m8 format of the same blast result I get:

Use of uninitialized value in warn at ./visualizeBlastHitsToChr.plx line 34, <DATA> line 192.
parsed ()

Is this a bug or am I doing something wrong? The blasttable looks like this:

x     y       97.23   5551    151     3       10336919        10342466        19011   13461   0.0     9759
x     y       94.04   5116    242     28      10345540        10350607        10402   5302    0.0     7438
x     y       94.22   1798    95      6       10353080        10354875        2902    1112    0.0     2698
x     y       97.48   1470    33      2       10344020        10345488        11922   10456   0.0     2609
x     y       96.82   1228    39      0       10342557        10343784        13388   12161   0.0     2125

Wrong place to post a bug I know... --DanBolser 15:22, 6 November 2008 (UTC)

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