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package Bio::GMOD::Bulkfiles::MyLargePrimarySeq;
use strict;
=head1 Bio::GMOD::Bulkfiles::MyLargePrimarySeq
patch to use Bio::Seq::LargePrimarySeq to read
feature locations from dna.raw files.
my $dnaseq= Bio::GMOD::Bulkfiles::MyLargePrimarySeq->new( -file => $dnafile);
$loc= new Bio::Location::something(...);
$bases= $dnaseq->subseq($loc);
=cut
use Bio::Seq::LargePrimarySeq;
use base qw(Bio::Seq::LargePrimarySeq);
#use vars qw(@ISA); BEGIN{ @ISA = qw(Bio::Seq::LargePrimarySeq); }
sub new {
my ($class, %params) = @_;
my $dnafile = delete $params{'-file'} ;
my $self = $class->SUPER::new(%params);
$self->dnafile($dnafile);
if( $dnafile && -e $dnafile ) {
## $self->_filename($dnafile); # don't change to our name in case StUPER wants to unlink it
my $fh= new FileHandle($dnafile);
$fh->seek(0,2);
my $flen= $fh->tell();
$fh->seek(0,0);
$self->_fh($fh);
$self->length($flen);
}
return $self;
}
sub dnafile {
my $self = shift;
if (@_) { $self->{dnafile}= shift; }
return $self->{dnafile};
}
## dang this nasty -- DONT unlink
sub DESTROY {
my $self = shift;
my $fh = $self->_fh();
close($fh) if( defined $fh );
$self->_filename(''); # is unlink '' bad ?
# this should be handled by Tempfile removal, but we'll unlink anyways.
##unlink $self->_filename() if defined $self->_filename() && -e $self->_filename;
##$self->SUPER::DESTROY();
}
#-------
1;
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