1: #!/usr/bin/perl -w 2: 3: use strict; 4: use Bio::DB::GenBank; 5: use Bio::SeqIO; 6: use File::Basename; 7: 8: # configuration information 9: my $outfile = 'outfile'; 10: my $progname = basename $0; 11: 12: # usage information 13: my $usage = "usage: $0 accession1 [accession2 ...]\n"; 14: die $usage unless @ARGV; 15: 16: # start program flow 17: my $gb = new Bio::DB::GenBank( 18: -retrievaltype => 'tempfile', 19: -format => 'Fasta' 20: ); 21: 22: my $seqout = Bio::SeqIO->new( -file => ">$outfile", -format => 'FASTA' ); 23: 24: my $seqio = $gb->get_Stream_by_acc( @ARGV ); 25: while( my $sequence = $seqio->next_seq ) { 26: $seqout->write_seq($sequence); 27: }
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Re: Fetching Biological Sequences from the NCBI
by Sameet (Beadle) on Apr 23, 2004 at 18:25 UTC |
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