Temporary utility to dump xref sequences to a FASTA file. Needed for...

Temporary utility to dump xref sequences to a FASTA file. Needed for development/debugging of xref mapping system.

misc-scripts/xref_mapping/xref_dumper.pl

+# Dump primary xrefs to FASTA file
+
+use strict;
+use DBI;
+
+my $file = "xref_dna.fasta";
+
+my $host = "ecs1g";
+my $port = 3306;
+my $database = "glenn_test_xref";
+my $user = "ensadmin";
+my $password = "ensembl";
+
+my $dbi = DBI->connect("dbi:mysql:host=$host;port=$port;database=$database",
+		       "$user",
+		       "$password",
+		       {'RaiseError' => 1}) || die "Can't connect to database";
+
+open(FILE, ">" . $file);
+
+my $sth = $dbi->prepare("SELECT x.xref_id, px.sequence FROM primary_xref px, source so, xref x, species sp WHERE sp.name='homo_sapiens' AND so.name='RefSeq' AND x.species_id=sp.species_id AND px.source_id=so.source_id AND x.xref_id=px.xref_id AND px.sequence_type='dna' LIMIT 100");
+$sth->execute();
+
+my ($xref_id, $sequence);
+$sth->bind_columns(\$xref_id, \$sequence);
+
+while (my @row = $sth->fetchrow_array()) {
+
+  print FILE ">$xref_id\n$sequence\n";
+
+}
+
+close(FILE);
+