Added a loading script for Ewan

misc-scripts/anopheles_scripts/load_dna.pl

+use strict;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::SeqIO;
+use Bio::EnsEMBL::DBSQL::ProteinAdaptor;
+
+use Bio::EnsEMBL::Utils::Eprof('eprof_start','eprof_end','eprof_dump');
+
+my $host      = 'ecs1b';
+my $dbuser    = 'ensadmin';
+my $dbname    = 'drosophila_melanogaster_9_3';
+my $dbpass    = 'ensembl';
+my $path      = 'FLYBASE';
+
+print STDERR "Connecting to $host, $dbname\n";
+
+
+my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
+					    '-host'   => $host,
+					    '-user'   => $dbuser,
+					    '-dbname' => $dbname,
+					    '-pass'   => $dbpass,
+					   );
+
+my ($dna) = @ARGV;
+
+my $in  = Bio::SeqIO->new(-file => $dna, '-format' =>'Fasta');
+my $count = 1;
+my $total = 0;
+while( (my $seq = $in->next_seq ) ) {
+    my $internal_count = 1;
+    $total++;
+    my $sequence = $seq->seq;
+    my $length = length($sequence);
+    my $ac = $seq->id;
+
+    my $clone = $total;
+    my $chr_id = $clone;
+
+#Load chromosome table
+    my $chrsth = $db->prepare('insert into chromosome (chromosome_id,name,length) values (?,?,?)');
+    $chrsth->execute(
+		     $chr_id,
+		     $ac,
+		     $length
+		     );
+    
+
+#Load clone table    
+        my $sth = $db->prepare('insert into clone (clone_id,name, embl_acc, version, embl_version, htg_phase, created, modified) values(?, ?, ?, ?, ?, ?,NOW(), NOW())'); 
+       
+    
+    $sth->execute(
+		  $clone,
+		  $ac,
+		  'NULL',
+		  1,
+		  0,
+		  3
+		  );
+		    
+    
+    my $div = int($length/25000);
+    my $l = int ($length/$div);
+    
+    print STDERR "AC: $ac\tDIV: $div\tL: $l\n";
+    
+    my $prev_end;
+
+    while ($internal_count <= $div) {
+
+	my $total_length;
+	if ($internal_count == 1) {
+	    
+	    my $actmp = $ac."_1";
+	    my $t = $l;
+#	    print STDERR  "AC: $actmp\nAC_CONTIG: $count\nDIV: $count\n";
+#	    print STDERR  "$actmp\t$prev_end\t$length\n";
+	    
+	    my $subseq = $seq->subseq(1,$l);
+	    my $subseql = length($subseq);
+	    $total_length = $total_length + $subseql;
+	    
+	    print STDERR "SUB: $subseql\tL: $l\n";
+	    
+#Load DNA table
+		my $statement = $db->prepare("
+        insert into dna(sequence,created) 
+        values(?, NOW())
+        "); 
+	    
+		my $rv = $statement->execute($subseq); 
+	
+    
+#Load contig table
+		
+		my $sth = $db->prepare("
+        insert into contig(name, contig_id, dna_id, length, clone_id, embl_offset) 
+        values(?, ?, ?, ?, ?, ?)
+        "); 
+	
+		my $rv = $sth->execute(
+				       $actmp,
+				       $count,
+				       $count,
+				       $subseql,
+				       $clone,
+				       1,
+				       );  
+
+#Load the assembly table
+
+	my $sth = $db->prepare("insert into assembly (chromosome_id,chr_start,chr_end,superctg_name,superctg_start,superctg_end,superctg_ori,contig_id,contig_start,contig_end,contig_ori,type) values (?,?,?,?,?,?,?,?,?,?,?,?)");
+	$sth->execute(
+		      $chr_id,
+		      1,
+		      $t,
+		      "FPC_".$ac,
+		      1,
+		      $t,
+		      1,
+		      $count,
+		      1,
+		      $t,
+		      1,
+		      "FLYBASE"
+		      
+		      );
+
+	    $count++;
+	    $prev_end = $l+1;
+	    $internal_count++;
+	}
+    
+
+
+	if (($internal_count > 1) && ($internal_count < $div)) {
+	    my $end = $prev_end + $l;
+	    my $subseq = $seq->subseq($prev_end,$end);
+	    my $subseql = length($subseq);
+	
+	    my $t = $l + 1;
+
+	    $total_length = $total_length + $subseql;
+
+	    my $actmp = $ac."_".$count;
+	
+	    #print STDERR  "AC: $actmp\nAC_CONTIG: $count\nDIV: $count\n";
+	    #print STDERR  "$actmp\t$prev_end\t$length\n";
+
+
+	       #Load DNA table
+		my $statement = $db->prepare("
+        insert into dna(sequence,created) 
+        values(?, NOW())
+        "); 
+	    
+		my $rv = $statement->execute($subseq); 
+	
+    
+#Load contig table
+		
+		my $sth = $db->prepare("
+        insert into contig(name, contig_id, dna_id, length, clone_id, embl_offset) 
+        values(?, ?, ?, ?, ?, ?)
+        "); 
+	
+		my $rv = $sth->execute(
+				       $actmp,
+				       $count,
+				       $count,
+				       $subseql,
+				       $clone,
+				       1,
+				       ); 
+	    
+	    print STDERR "SUB: $subseql\tL: $l\n";
+
+	    my $sth = $db->prepare("insert into assembly (chromosome_id,chr_start,chr_end,superctg_name,superctg_start,superctg_end,superctg_ori,contig_id,contig_start,contig_end,contig_ori,type) values (?,?,?,?,?,?,?,?,?,?,?,?)");
+	$sth->execute(
+		      $chr_id,
+		      $prev_end,
+		      $end,
+		      "FPC_".$ac,
+		      $prev_end,
+		      $end,
+		      1,
+		      $count,
+		      1,
+		      $t,
+		      1,
+		      "FLYBASE"
+		      
+		      );
+
+	    
+
+	    $prev_end = $end+1;
+	    $internal_count++;
+	    $count++;
+
+	}
+	
+	if ($internal_count == $div) {
+	    
+	    my $actmp = $ac."_".$count;
+	    my $subseq = $seq->subseq($prev_end,$length);
+	    my $subseql = length($subseq);
+	    
+	    my $t = $l + 1;
+	   
+	    $total_length = $total_length + $subseql;
+
+#	    print STDERR  "AC: $actmp\nAC_CONTIG: $count\nDIV: $count\n";
+#	    print STDERR  "$actmp\t$prev_end\t$length\n";
+		
+	       #Load DNA table
+		my $statement = $db->prepare("
+        insert into dna(sequence,created) 
+        values(?, NOW())
+        "); 
+	    
+		my $rv = $statement->execute($subseq); 
+	
+    
+#Load contig table
+		
+		my $sth = $db->prepare("
+        insert into contig(name, contig_id, dna_id, length, clone_id, embl_offset) 
+        values(?, ?, ?, ?, ?, ?)
+        "); 
+	
+		my $rv = $sth->execute(
+				       $actmp,
+				       $count,
+				       $count,
+				       $subseql,
+				       $clone,
+				       1,
+				       ); 
+
+	    my $sth = $db->prepare("insert into assembly (chromosome_id,chr_start,chr_end,superctg_name,superctg_start,superctg_end,superctg_ori,contig_id,contig_start,contig_end,contig_ori,type) values (?,?,?,?,?,?,?,?,?,?,?,?)");
+	$sth->execute(
+		      $chr_id,
+		      $prev_end,
+		      $length,
+		      "FPC_".$ac,
+		      $prev_end,
+		      $length,
+		      1,
+		      $count,
+		      1,
+		      $subseql,
+		      1,
+		      "FLYBASE"
+		      
+		      );
+
+	    $count++;
+	    $internal_count++;
+	    if ($total_length =! $l) {
+		print STDERR  "TOTAL: $total_length\nLENGTH: $length\n";
+		die;
+	    }
+	}
+    }
+}
+    
+
+
+
+