[Bioperl-l] Bioperl and ACE files

Wes Barris wes.barris at csiro.au
Mon Feb 16 01:33:02 EST 2004


I have an ACE file that I am trying to process with bioperl.  A portion
of the ACE file looks like this:

AF CB429506 U 2
AF CB428704 U 6
AF CB430643 U 1
AF CB431187 U 0
AF CB430639 U -7
AF CB430480 C 24
AF CB430055 U 10

Notice the line in the middle that shows a starting position of '0'
(zero)?  When bioperl tries to process this sequence, an error is
thrown.  I have found the port of the bioperl code that throws the
sub get_nse{
    my ($self,$char1,$char2) = @_;

    $char1 ||= "/";
    $char2 ||= "-";

    $self->throw("Attribute id not set") unless $self->id();
    $self->throw("Attribute start not set") unless $self->start();<-----
    $self->throw("Attribute end not set") unless $self->end();

    return $self->id() . $char1 . $self->start . $char2 . $self->end ;


Notice how "$self->start()" is tested.  When it encounters a sequence
whose start is set to zero, an error is thrown.

I don't know much about the ACE file format.  Do I have a questionable
ACE file or is this test incomplete?
Wes Barris
E-Mail: Wes.Barris at csiro.au

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