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bin/bp_genbank2gff  view on Meta::CPAN

			   @dsn,
			   @auth,
			   -preferred_tags => \%preferred_tags,
			   -source=> $SOURCE || 'Genbank')
  or die "Can't open database: ",Bio::DB::GFF->error,"\n";

if ($CREATE) {
  $db->initialize(1);
}

die "you must specify either an accession to retrieve from\nembl or a local file containing data in embl format\n" if (($FILE || $ACC) && !scalar(@ARGV));

if ($ACC) {
  while ($_ = shift) {
    status(loading => $_);
    my $result = $db->load_from_embl(/^NC_/?'refseq':'embl' => $_);
    status(done    => $result);
  }
  exit 1;
}

lib/Bio/DB/GFF.pm  view on Meta::CPAN

  my $self              = shift;
  my $file_or_directory = shift || '.';
  my $verbose           = shift;

  local $self->{__verbose__} = $verbose;
  return $self->do_load_gff($file_or_directory) if ref($file_or_directory)
                                                   && tied *$file_or_directory;

  my $tied_stdin = tied(*STDIN);
  open my $SAVEIN, "<&STDIN" unless $tied_stdin;
  local @ARGV = $self->setup_argv($file_or_directory,'gff','gff3') or return;  # to play tricks with reader
  my $result = $self->do_load_gff('ARGV');
  open STDIN, '<', $SAVEIN unless $tied_stdin;  # restore STDIN
  return $result;
}

*load = \&load_gff;

=head2 load_gff_file

 Title   : load_gff_file

lib/Bio/DB/GFF.pm  view on Meta::CPAN

  my $self              = shift;
  my $file_or_directory = shift || '.';
  my $verbose           = shift;

  local $self->{__verbose__} = $verbose;
  return $self->load_sequence($file_or_directory) if ref($file_or_directory)
                                                     && tied *$file_or_directory;

  my $tied = tied(*STDIN);
  open my $SAVEIN, "<&STDIN" unless $tied;
  local @ARGV = $self->setup_argv($file_or_directory,'fa','dna','fasta') or return;  # to play tricks with reader
  my $result = $self->load_sequence('ARGV');
  open STDIN, '<', $SAVEIN unless $tied;  # restore STDIN
  return $result;
}


=head2 load_fasta_file

 Title   : load_fasta_file
 Usage   : $db->load_fasta_file($file [,$verbose]);