branch-1-6/examples/db/getGenBank.pl

   1 #!/usr/local/bin/perl -w
   2 #
   3 # How to retrieve GenBank entries over the Web
   4 #
   5 # by Jason Stajich
   6 #
   7 use Bio::DB::GenBank;
   8 use Bio::SeqIO;
   9 my $gb = new Bio::DB::GenBank;
  10
  11 # the output stream for your seqs, this can be a file
  12 # instead or STDOUT, see the Bio::SeqIO module for info
  13
  14 my $seqout = new Bio::SeqIO(-fh => \*STDOUT, -format => 'fasta');
  15
  16 # if you want a single seq
  17 my $seq = $gb->get_Seq_by_id('MUSIGHBA1');
  18 $seqout->write_seq($seq);
  19 # or by accession
  20 $seq = $gb->get_Seq_by_acc('AF303112');
  21
  22 $seqout->write_seq($seq);
  23
  24 # feel free to pull multiple sequences...
  25 # if you want to get a bunch of sequences use the get_Stream_by_id/acc methods
  26 my $seqio = $gb->get_Stream_by_id([ qw(J00522 AF303112 2981014)]);
  27
  28 while( defined ($seq = $seqio->next_seq )) {
  29         $seqout->write_seq($seq);
  30 }