[Bioperl-guts-l] [Bug 1642] New: Bio::DB::Flat.pm failure to instantiate correct DB sequence format

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.bioperl.org/show_bug.cgi?id=1642

           Summary: Bio::DB::Flat.pm failure to instantiate correct DB
                    sequence format
           Product: Bioperl
           Version: main-trunk
          Platform: Macintosh
        OS/Version: MacOS X
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: jeffrey.barrick at yale.edu


If you create a Flat database of genbank sequences that uses BinarySearch.pm, sequences read 
from the database are created in FASTA format instead.  There is a breakdown in passing the 
format read form the database configuration file in Flat.pm to BinarySearch.pm that makes it revert 
to the default format.

The problem is around line 178, in this code segment:

  # because Michele and Lincoln did it differently
  # Michele's way is via a standalone concrete class
  if ($index_type eq 'Binary') {
    my $child_class = 'Bio::DB::Flat::BinarySearch';
    eval "use $child_class";
    $self->throw($@) if $@;
    return $child_class->new(@_);
  }

---
Adding -format to the arguments corrects the problem:

  # because Michele and Lincoln did it differently
  # Michele's way is via a standalone concrete class
  if ($index_type eq 'Binary') {
    my $child_class = 'Bio::DB::Flat::BinarySearch';
    eval "use $child_class";
    $self->throw($@) if $@;
    push @_, ('-format', $format);
    return $child_class->new(@_);
  }

---

There might be some other values that it intends to pass as well.



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