From 3a3dd37c9a391f47cde0faf17e7c1264458737ea Mon Sep 17 00:00:00 2001
From: Emmanuel Mongin <mongin@sanger.ac.uk>
Date: Thu, 2 Jan 2003 11:43:47 +0000
Subject: [PATCH] Added a loading script for Ewan
---
misc-scripts/anopheles_scripts/load_dna.pl | 271 +++++++++++++++++++++
1 file changed, 271 insertions(+)
create mode 100644 misc-scripts/anopheles_scripts/load_dna.pl
diff --git a/misc-scripts/anopheles_scripts/load_dna.pl b/misc-scripts/anopheles_scripts/load_dna.pl
new file mode 100644
index 0000000000..f878dcd624
--- /dev/null
+++ b/misc-scripts/anopheles_scripts/load_dna.pl
@@ -0,0 +1,271 @@
+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;
+ }
+ }
+ }
+}
+
+
+
+
+
--
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