Added test_genes which just fetches genes from the database

Added overlap_test which tests VirtualContig and ContigOverlap

scripts/clone2flat.pl

@@ -276,11 +276,8 @@ foreach my $clone_id ( @clones ) {
 
     eval {
 	my $clone = $db->get_Clone($clone_id);
-	print(STDERR "ick\n");
 	my $as    = $clone->virtualcontig;
-	print(STDERR "wor\n");
 	$as->skip_SeqFeature('similarity',1);
-	print(STDERR "pog\n");
 	# choose output mode
 	
 	# test clone check call
@@ -292,7 +289,7 @@ foreach my $clone_id ( @clones ) {
 	    }
 	}
 
-	my $debug = 1;
+	my $debug = 0;
 	if($debug){
 	    # debug tests
 	    my $id=$clone->id;
@@ -308,7 +305,7 @@ foreach my $clone_id ( @clones ) {
 	    }
 	    exit 0;
 	}
-
+        print(STDERR "Format is $format\n");
 	if( $format =~ /gff/ ) {
 	    foreach my $contig ( $clone->get_all_Contigs )  {
 		my @seqfeatures = $contig->as_seqfeatures();

scripts/overlap_test

@@ -5,7 +5,7 @@ use Bio::EnsEMBL::DB::VirtualContig;
 
 my $db = new Bio::EnsEMBL::DBSQL::Obj(-host   => 'obi-wan',
 				      -port   => 410000,
-				      -dbname => 'ens500',
+				      -dbname => 'ens500a',
 				      -user => 'ensro',
 				      );
 

scripts/test_genes

+#!/usr/local/bin/perl
+
+use strict;
+
+use Bio::EnsEMBL::DBLoader;
+use Bio::EnsEMBL::DBSQL::Obj;
+use Bio::EnsEMBL::AceDB::Obj;
+use Getopt::Long;
+use Time::Local;
+
+my $dbtype1 = 'rdb';
+my $host1   = 'obi-wan';
+my $dbname1 = 'ens500';
+my $dbuser1 = 'ensro';
+my $dbpass1 = undef;
+my $port1   = 3306;
+
+my $infile  = '';
+$| = 1;
+&GetOptions( 'dbtype1:s'  => \$dbtype1,
+	     'host1:s'    => \$host1,
+	     'port1:n'    => \$port1,
+	     'dbname1:s'  => \$dbname1,
+	     'dbpass1:s'  => \$dbpass1,
+	     'infile=s'   => \$infile,
+	     );
+
+my ($db1) = get_db_handles();
+
+my ($clone1) = get_cloneids($infile,@ARGV);
+my $i = 0;
+
+for ($i = 0; $i <= $#$clone1; $i++) {
+    print("Processing clone " . $clone1->[$i] . "\n");
+    eval {
+    my $cl1    = $db1->get_Clone($clone1->[$i]);
+
+    my @genes1 = $cl1->get_all_Genes();
+
+    my $count = 1;
+
+    foreach my $gene1 (@genes1) {
+        foreach my $exon ($gene1->each_unique_Exon) {
+                print("Exon " . $exon->id . "\t" .$exon->start . "\t" . $exon->end . "\t" . $exon->strand . "\n");
+	    }
+    }
+}
+
+sub get_cloneids {
+    my ($infile,@ARGV) = @_;
+
+    my @clone1;
+
+    if (defined($infile)) {
+	open(IN,"<$infile");
+	while (<IN>) {
+	    chomp;
+	    push(@clone1,$_);
+	}
+	close(IN);
+    }
+    while ($#ARGV > 0) {
+	my $clone1 = shift @ARGV;
+	push(@clone1,$clone1);
+    }
+    return (\@clone1);
+}
+
+
+
+sub get_db_handles {
+    my ($db1);
+
+    if( $dbtype1 =~ 'ace' ) {
+	$db1 = Bio::EnsEMBL::AceDB::Obj->new( -host => $host1, 
+					      -port => $port1);
+    } elsif ( $dbtype1 =~ 'rdb' ) {
+
+	my $locator = "Bio::EnsEMBL::DBSQL::Obj/host=$host1;" .
+  	              "port=$port1;"      .
+		      "dbname=ensembl;"  .
+		      "user=$dbuser1;"    .
+		      "pass=$dbpass1";
+
+	$db1 = Bio::EnsEMBL::DBLoader->new($locator);
+	
+    } else {
+	die("$dbtype1 is not a good type (should be ace or rdb)");
+
+    }
+
+    return ($db1);
+}