its a start but needs alot more work

misc-scripts/assembly_patches/README.TXT

+#Get the sequence data. Should be able to down load fasta later but for now do it manually.
+
+mfetch -d embl -v fasta AC093223.3 AC145145.2 AC144587.2 AC142525.2 AC139494.2 AC118459.2 AC139500.2 AC108108.2 AC138827.3 AC146335.1 AC139463.2 AC138832.2 > seq.fasta
+
+
+Get the mappings
+
+In Genome workbench click on Patch Scaffolds and export agp.
+to get hap -> contig
+
+See file thjat was attached to get ref->hap mappings.
+
+
+NOW use....
+-----------
+
+ wget ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/PATCHES/patch_release_1/FASTA/alt.scaf.fa.gz
+gunzip alt.scaf.fa.gz
+
+ wget ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/PATCHES/patch_release_1/alt_scaffold_placement.txt
+
+wget ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/PATCHES/patch_release_1/AGP/alt.scaf.agp.gz
+gunzip alt.scaf.agp.gz
+
+
+

misc-scripts/assembly_patches/schema_patch_load.pl

+use Bio::EnsEMBL::Registry;
+use strict;
+
+my $pass         = shift;
+my $fasta_file   = shift || "alt.scaf.fa";
+my $mapping_file = shift || "alt.scaf.agp";
+my $txt_file     = shift || "alt_scaffold_placement.txt";
+
+my $dbname = shift || "ianl_homo_sapiens_core_57_37b";
+my $host   = "ens-research";
+my $user   = "ensadmin";
+
+#connect to the database
+
+  my $dba = new Bio::EnsEMBL::DBSQL::DBAdaptor(
+    '-host'    => $host,
+    '-user'    => $user,
+    '-pass'    => $pass,
+    '-dbname'  => $dbname,
+    '-species' => "load"
+  );
+
+#Load fasta sequences first. Keep a record of the first so that if things
+#go wrong we can delete what has already been done.
+
+my $sth = $dba->dbc->prepare("select max(seq_region_id) from seq_region")
+  || die "Could not get max seq_region_id";
+
+
+$sth->execute || die "priblkem executing";
+my $max_seq_region_id;
+$sth->bind_columns(\$max_seq_region_id) || die "problem binding";
+$sth->fetch() || die "problem fetching";
+$sth->finish;
+
+
+$max_seq_region_id++;
+my $start_seq_region_id = $max_seq_region_id;
+
+print "starting new seq_region at seq_region_id of $max_seq_region_id\n";
+print "\nTo reset\ndelete from dna where seq_region_id >= $start_seq_region_id\ndelete from seq_region where seq_region_id >= $start_seq_region_id\n\n";
+
+my ($chr_coord_id, $contig_coord_id);
+
+$sth = $dba->dbc->prepare('select coord_system_id from coord_system where name like ? and attrib like "%default_version%"')
+  || die "Could not prepare coord_system sql";
+
+$sth->execute("chromosome") || die "Could not execute coord_system sql";
+$sth->bind_columns(\$chr_coord_id) || die "What a bind NOT";
+$sth->fetch() || die "Could not fetch coord_system_id";
+
+$sth->execute("contig") || die "Could not execute coord_system sql";
+$sth->bind_columns(\$contig_coord_id) || die "What a bind NOT";
+$sth->fetch() || die "Could not fetch coord_system_id";
+$sth->finish;
+
+
+my $get_seq_region_sth = $dba->dbc->prepare("select seq_region_id, length from seq_region where name like ?")
+  || die "Could not prepare get_seq_region";
+
+
+my $insert_seq_region_sth = $dba->dbc->prepare("insert into seq_region (seq_region_id, name, coord_system_id, length) values(?, ?, ?, ?)") || die "Could not prepare seq_region insert sql";
+
+my $insert_dna_sth =  $dba->dbc->prepare("insert into dna (seq_region_id, sequence) values (?, ?)")
+  || die "Could not prepare insert dna sql";
+
+
+if(!defined($chr_coord_id) or !defined($contig_coord_id)){
+  die "No coord_system_id for chromosome ($chr_coord_id) or contig ($contig_coord_id)\n";
+}
+
+#      Store contigs as seq_region + dna.
+
+open(FASTA, "<".$fasta_file)    || die "Could not open file $fasta_file";
+open(MAPPER,"<".$mapping_file)  || die "Could not open file $mapping_file";
+
+my $seq = "";
+my $name = undef;
+my $version = 0;
+my %name2id;
+
+while(<FASTA>){
+  chomp;
+  if($_ =~ /^>(\S*)/){
+#    print $1."\t".$2."\n";
+    if(defined($name)){
+      load_seq_region($name, \$seq);
+    }
+    $name = $1;
+    $version = $2;
+    $seq = "";
+  }	
+  else{
+    $seq .= $_;
+  }
+}
+
+if(defined($name)){
+  load_seq_region($name, \$seq);
+}
+
+close FASTA;
+
+
+#      Create haplotype seq_region (calulate length from mapping data)
+while(<MAPPER>){
+  next if($_ ~= /^#/); #ignore comemnts
+}	
+
+# add mappings
+
+#      First the ref -> haplotype mappings
+#      Then haplo -> contig mappings
+
+# create haplotype in assembly_exception
+
+
+#Do these things just have names or versions too?
+
+
+sub load_seq_region{
+  my $name = shift;
+  my $seq =  shift;
+
+  my ($tmp_id,$tmp_len);
+  $get_seq_region_sth->execute($name)
+    || die "Could not execute get seq_region for $name";
+  $get_seq_region_sth->bind_columns(\$tmp_id,\$tmp_len)
+    || die "Could not bind get_seq_region";
+  $get_seq_region_sth->fetch();
+#    || die "Could not fetch seq_region id for name $name";;
+
+  if(defined($tmp_id)){
+    if($tmp_len == length($$seq)){
+      print "seq region $name already found and in database\n";
+      $name2id{$name} = $tmp_id;
+      return;
+    }
+    die "Seq region found for $name but not the same length. In datatabse length = $tmp_len and in the new fasta file ".length($$seq);
+  }
+  print "adding new seq region $name length of sequence = ".length($$seq)."\n";
+
+  $insert_seq_region_sth->execute($max_seq_region_id, $name, $contig_coord_id, length($$seq))
+    || die "Could not insert seq region for $name";
+  $insert_dna_sth->execute($max_seq_region_id, $seq)
+    || die "Could not add seq for $name";
+
+  $name2id{$name} = $max_seq_rgion_id;
+
+  $max_seq_region_id++;
+
+  return;
+}