--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getdata/get_gb_sp.pl	Tue Mar 11 12:19:13 2014 -0700
@@ -0,0 +1,68 @@
+#!/usr/bin/perl
+use strict;
+no warnings; #genbank produces annoying warning if no sequence is found
+
+#use FindBin;
+#use lib "$FindBin::Bin/lib";
+use Bio::DB::GenBank;
+use Bio::SeqIO;
+use Bio::Root::Exception;
+use Error qw(:try);
+
+
+my $datafile = $ARGV[0];
+my $datatype = $ARGV[1];
+my $outtype = $ARGV[2];
+my $outfile = $ARGV[3];
+my $nodata = $ARGV[4];
+
+my $accessions;
+my @accnums;
+
+	open (FILE,"<$datafile") or die "Cannot open file containing accession numbers\n";
+	open (OUT,">$outfile") or die "Cannot open outfile\n";
+	close OUT; #This overwrites old file if it exists
+	open (ND,">$nodata") or die "Cannot open file\n";
+	my $fh = Bio::SeqIO->newFh(-format=>$outtype, -file=>">>$outfile");
+
+
+	while (<FILE>)
+	{
+	        chomp;
+	        next unless ($_);
+		push(@accnums, $_);
+	}
+	close FILE;
+
+	my $countnames = 0;
+	foreach (@accnums){
+		#Should check input for one word per line and throw error if not, which is not done
+	
+	        $accessions = $_;
+		chomp;
+		if($accessions eq ""){
+			die "Put spaces between accession numbers. No Empty Lines allowed.\n";
+		}
+	        my $qry_string .= $accessions."[organism]"." ";
+	
+#	        my $GBseq;
+	        my $gb = new Bio::DB::GenBank;
+	        my $query = Bio::DB::Query::GenBank->new
+	                (-query   =>$qry_string,
+	                 -db      =>$datatype);
+
+		my $seqio;
+
+		if (eval {$gb->get_Stream_by_query($query)}){
+			$seqio = $gb->get_Stream_by_query($query);
+			while( my $GBseq = $seqio->next_seq ) {
+				my $sequence = $GBseq;   # read a sequence object
+				print $fh $sequence; # write a sequence object
+			}
+		}else{
+			print ND "$accessions\n";
+		}
+	}
+exit;
+
+