[Bioperl-l] parsing blast XML reports with Bio::SearchIO

[Jonathan Flowers]

Hi,

I am trying to parse BLAST reports written in XML using Bio::SearchIO. When
running the following code on a set of reports (multiple query results in a
single file), I only get one ResultI object.  I tried running the same code
on a file in 'blast' format and obtained the expected results (ie one
ResultI object for each query), suggesting that the issue is with blastxml.
I found an old thread on this listserv where someone had had a similar
problem, but could not find how it was resolved.

I am using Bioperl 1.5.2 and the XML reports were generated using blastall
with the -m7 option.

my $in = new Bio::SearchIO(-format => 'blastxml',  -file   =>
'blastreport.xml' );
while( my $result = $in->next_result ) {
            print $result->query_name,"\n";
      while( my $hit = $result->next_hit ) {
              while( my $hsp = $hit->next_hsp ) {
                     #do something with hsp
              }
      }
}

Thanks

Jonathan