--- /dev/null
+#!/usr/bin/perl -w
+
+use DBI;
+
+$SIG{__WARN__} = sub { die @_ };
+
+my $mysql = DBI->connect("DBI:mysql:database=seq_demo;user=seq_demo;password=demo_pass");
+
+$mysql->do(q{LOCK TABLES prot WRITE,
+ annot WRITE,
+ sp WRITE });
+
+my $EL = 125;
+my $NA = 123;
+
+my @aatrans = ($EL,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$EL,$NA,$NA,$EL,$NA,$NA,
+ $NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,
+ $NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA, 24,$NA,$NA,$NA,$NA,$NA,
+ $NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,$NA,
+ $NA, 1, 21, 5, 4, 7, 14, 8, 9, 10,$NA, 12, 11, 13, 3,$NA,
+ 15, 6, 2, 16, 17,$NA, 20, 18, 23, 19, 22,$NA,$NA,$NA,$NA,$NA,
+ $NA, 1, 21, 5, 4, 7, 14, 8, 9, 10,$NA, 12, 11, 13, 3,$NA,
+ 15, 6, 2, 16, 17,$NA, 20, 18, 23, 19, 22,$NA,$NA,$NA,$NA,$NA
+ );
+
+my $ins_prot = $mysql->prepare(q{
+ INSERT INTO prot (seq,bin,len) VALUES (?, ?, ?)
+ });
+
+my $ins_annot = $mysql->prepare(q{
+ INSERT INTO annot (gi, prot_id, db, descr) VALUES (?, ?, ?, ?)
+ });
+
+my $ins_sp = $mysql->prepare(q{
+ INSERT INTO sp (gi, acc, name) VALUES (?, ?, ?)
+ });
+
+use vars qw( $seq $bin $tot_seq $tot_annot $tot_sp );
+use vars qw( $gi $prot_id $db $desc $sp_acc $sp_name );
+use vars qw( $header $seq @entries );
+use vars qw( $gi $db $db_acc $db_name $desc);
+
+$tot_seq = $tot_annot = $tot_sp = 0;
+
+for my $db_file ( @ARGV ) {
+ open(DATA, "<$db_file") or die $!;
+ local $/ = "\n>";
+ while (<DATA>) {
+ chomp; # remove trailing "\n>" record header
+ ($header, $seq) = $_ =~ m/^>? # record separator (first entry)
+ ( [^\n]* ) \n # header line
+ ( .* ) # the sequence
+ /osx; # optimize, multiline, commented
+
+ $seq =~ s/\W|\d//sg;
+ $bin = pack('C*', map { $aatrans[unpack('C', $_)] } split(//, $seq));
+ $ins_prot->execute($seq,$bin,length($seq));
+ $prot_id = $ins_prot->{mysql_insertid};
+
+ $tot_seq++;
+
+# print STDERR "Inserted $prot_id: ". length($seq)."\n";
+
+ @entries = split(/\001/, $header);
+
+ for ( @entries ) {
+ ($gi,$db,$db_acc,$db_name,$desc)=
+ $_ =~ /^gi\|(\d+)\|([a-z]+)\|(\S*)\|(\S*) (.*)$/o;
+# print "$prot_id: $gi\t$db\t$db_acc\t$desc\n";
+ $ins_annot->execute($gi,$prot_id,$db,$desc);
+
+ $tot_annot++;
+
+ if ($db eq "sp") {
+ $ins_sp->execute($gi,$db_acc,$db_name);
+ $tot_sp++;
+ }
+ }
+ }
+ close(DATA);
+}
+
+print "Inserted $tot_seq sequences; $tot_annot annotations; $tot_sp swissprot\n";
+
+
+