[Bioperl-guts-l] [Bug 2686] New: WU-BLAST XML support

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Tue Nov 25 16:45:17 EST 2008


           Summary: WU-BLAST XML support
           Product: BioPerl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: sandain at hotmail.com

Regular expressions in the Bio::SearchIO::blastxml package are too specific in
the _chunk_normalblast method to work with WU-BLAST 2.0 xml output (mformat=7
option).  I have a patch for the current HEAD (rev 14987) available to fix this

Output created with the xmlcompact option is not parsed because no line feeds
are included.  I was unable to figure out a patch that wouldn't break anything,
so I currently just preparse the file with the following code:

my $fh = IO::File->new($ARGV[0]);
my $tfh = IO::File->new_tmpfile or die "Unable to open temp file: $!";  
foreach my $line (<$fh>) {
  $line =~ s/></>\n</g;
  print $tfh $line;
my  $searchIO = new Bio::SearchIO(-format => 'blastxml', -fh => $tfh);

I sure there is a simple fix for this, but I don't know where best to look in
the current code base.

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