diff --git a/misc-scripts/assembly_patches/add_GRC_align_features.pl b/misc-scripts/assembly_patches/add_GRC_align_features.pl
new file mode 100755
index 0000000000000000000000000000000000000000..d53edb6531fca5ff0f0e3544b2921cae94e89078
--- /dev/null
+++ b/misc-scripts/assembly_patches/add_GRC_align_features.pl
@@ -0,0 +1,333 @@
+#!/usr/bin/env perl
+#
+# Adds GRC genomic mapping to the dna align feature table
+# in the HAP pipeline with their cigar strings. Note that
+# in some cases there is more than one alignment per patch.
+#
+# Example:
+#
+# perl add_GRC_align_features.pl -dbhost genebuildn \
+# -dbname homo_sapiens_core_nn_nn -dbuser user -dbpass pass \
+# -patch_release GRCh37.p8 -verbose
+
+use strict;
+use warnings;
+
+use Getopt::Long;
+use Net::FTP;
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use Bio::EnsEMBL::Slice;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::DBSQL::SliceAdaptor;
+use Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor;
+use Bio::EnsEMBL::AssemblyExceptionFeature;
+use Bio::EnsEMBL::DnaDnaAlignFeature;
+use Bio::EnsEMBL::Analysis;
+
+$| = 1;
+
+my $dbname = '';
+my $dbhost = '';
+my $dbuser = 'ensro';
+my $dbpass = '';
+my $dbport = '3306';
+my $patch_release = '';
+my $store = 0;
+my $external_db_id = '50692'; # GRC_alignment_import
+my $syn_external_db_id = '50710'; # seq_region_synonym slice type - i.e. INSDC
+
+my $verbose = 0;
+
+my @patch_types = ('PATCH_FIX','PATCH_NOVEL');
+my @dna_align_features = ();
+
+&GetOptions(
+ 'dbhost:s' => \$dbhost,
+ 'dbuser:s' => \$dbuser,
+ 'dbpass:s' => \$dbpass,
+ 'dbname:s' => \$dbname,
+ 'dbport:n' => \$dbport,
+ 'patch_release:s' => \$patch_release,
+ 'external_db_id:n' => \$external_db_id,
+ 'write!' => \$store,
+ 'verbose!' => \$verbose,
+);
+
+if(!$patch_release){
+ throw ("Need to specify assembly version with -patch_release.\n");
+}
+
+# get alt_scaffold_placement.txt to generate filename that we will need
+# to retrieve files from the NCBI ftp site. Populates...
+
+my %ftp_filename=();
+
+my ($content, $remote_file_handle) = "";
+open($remote_file_handle, '>', \$content);
+
+my $ftp = Net::FTP->new('ftp.ncbi.nlm.nih.gov', Debug => 0)
+ or die "Can't connect to NCBI FTP: $@";
+
+$ftp->login('anonymous', '-anonymous@')
+ or die 'Cannot login ', $ftp->message;
+
+chomp $patch_release;
+
+my $ncbi_wd =
+ "genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/".
+ $patch_release.
+ "/PATCHES/alt_scaffolds/";
+
+$ftp->cwd($ncbi_wd)
+ or die 'Cannot change working directory ', $ftp->message;
+
+$ftp->get('alt_scaffold_placement.txt', $remote_file_handle)
+ or die "get failed ", $ftp->message;
+
+my @asp_lines = split /\n/, $content;
+
+foreach my $asp_line (@asp_lines) {
+ next if $asp_line =~ /^#/;
+ my @elem = split /\t/, $asp_line;
+ my $patch_name = $elem[2];
+ my $file_name = $elem[3]."_".$elem[6].".gff";
+ print "Filename: $file_name\t\tPatchname: $patch_name\n" if $verbose;
+ $ftp_filename{$patch_name} = $file_name;
+}
+
+# change directory to where the GRC alignments are kept:
+
+$ncbi_wd = "alignments";
+$ftp->cwd($ncbi_wd) or die 'Cannot change working directory ', $ftp->message;
+
+# hash of arrays - there way be more than one alignment per file if they
+# have been manually annotated, However the GRC may change all to one
+# line in the near future, in the meantime, we need to deal with them.
+
+my %align_str =();
+
+foreach my $patch (keys %ftp_filename) {
+ close $remote_file_handle;
+ open($remote_file_handle, '>', \$content);
+ $ftp->get($ftp_filename{$patch}, $remote_file_handle)
+ or die "get failed ", $ftp->message;
+
+ my @lines = split "\n", $content;
+ foreach my $line (@lines) {
+ next if $line =~ /^\#/;
+ # We'll parse the data later because we need most of it.
+ push @{$align_str{$patch}},$line;
+ }
+ #sleep 1;
+}
+
+
+
+my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor( -host => $dbhost,
+ -user => $dbuser,
+ -pass => $dbpass,
+ -port => $dbport,
+ -dbname => $dbname );
+
+my $sa = $db->get_SliceAdaptor();
+
+my $analysis = new Bio::EnsEMBL::Analysis( -logic_name => "grc_alignment_import",
+ -db_version => $patch_release);
+
+
+
+# TODO - leave $asm_exc_adaptor in - that way we can compare
+# information from file with what we already know as a sanity check.
+
+
+# Now get the patches, they come in pairs, the assembly exception and the reference
+print "Getting patches...\n" if $verbose;
+my $asm_exc_adaptor = $db->get_AssemblyExceptionFeatureAdaptor();
+my @exceptions = @{$asm_exc_adaptor->fetch_all()};
+my @patches;
+EXC: foreach my $exc (@exceptions){
+ foreach my $type (@patch_types){
+ if($exc->type() =~ m/$type/){
+ push(@patches, $exc);
+ next EXC;
+ }
+ }
+}
+# Assuming that AssemblyExceptionFeatureAdaptor's fetch_all will always
+# return 2 entries for each patch and that those two entries are adjacent
+my $num_patches = scalar(@patches)/2;
+
+print "Have ".$num_patches." patches.\n";
+
+# for each patch
+for (my $i = 0; $i < $num_patches; $i++) {
+
+ # get the two slices
+ my $ref_slice;
+ my $patch_slice;
+
+ for(my $j = 0; $j < 2; $j++) {
+ my $exc = pop(@patches);
+ # if this is the ref version
+ if($exc->type =~ m/REF/){
+ # alt is only the patch slice
+ $patch_slice = $exc->alternate_slice();
+ }
+ else{
+ # alt is replaced region of ref
+ $ref_slice = $exc->alternate_slice();
+ }
+ }
+ if(!($patch_slice and $ref_slice)){
+ throw("Something is wrong, the patch and ref slices were not set correctly.\n");
+ }
+
+ my @patch_vals = split /:/, $patch_slice->display_id;
+ my $patch_name = $patch_vals[2];
+
+ foreach my $string ( @{ $align_str{$patch_name}}) {
+ my @el = split /\t/, $string;
+
+ my $num = $#el;
+ throw ("Incorrect number of elements in gtf file: $num") unless $num == 8;
+
+ my ($seq_id, $source, $type, $start, $end, $score, $strand, $phase, $attr) = split /\t/, $string;
+
+ $strand = fix_strand($strand);
+
+ my %attribute = ();
+ foreach my $kvp (split ';', $attr) {
+ my ($key, $value) = split '=', $kvp;
+ $attribute{$key} = $value;
+ }
+
+ my $target = $attribute{"Target"};
+ my ($hseqname, $hstart, $hend, $hstrand ) = split " ", $target;
+
+ $hstrand = fix_strand($hstrand);
+
+ my $length = ($hend - $hstart) + 1;
+
+ my $cigar_line;
+ $cigar_line = $attribute{"Gap"};
+ if (defined $cigar_line) {
+ sanity_check_cigar_line($cigar_line, $length);
+ $cigar_line = reformat_cigar_line($cigar_line);
+ } else {
+ $cigar_line = $length."M";
+ }
+
+
+ # need the seq_region_id from seq_region_synonym
+ my @synonyms = @{$ref_slice->get_all_synonyms()};
+ my $seq_region_id = '';
+ foreach my $syn (@synonyms) {
+ if ($syn->external_db_id() == $syn_external_db_id) {
+ $seq_region_id = $syn->seq_region_id();
+ last();
+ }
+ }
+ # ...to obtain the slice:
+
+ my $slice = $sa->fetch_by_seq_region_id($seq_region_id);
+
+
+ my $daf = new Bio::EnsEMBL::DnaDnaAlignFeature(
+ -slice => $slice,
+ -start => $start,
+ -end => $end,
+ -strand => $strand,
+ -analysis => $analysis,
+ -score => $score,
+ -hstart => $hstart,
+ -hend => $hend,
+ -hstrand => $hstrand,
+ -hseqname => $hseqname,
+ -hcoverage => $attribute{"pct_coverage"},
+ -percent_id => $attribute{"pct_identity_ungap"},
+ -external_db_id => $external_db_id,
+ -cigar_string => $cigar_line,
+ );
+
+ push @dna_align_features, $daf;
+ }
+}
+
+
+# now store all the dna_align features
+if (scalar(@dna_align_features) > 0) {
+ write_dna_align_features_to_db($db,\@dna_align_features,$store)
+}
+print "There are ".scalar (@dna_align_features)." dna_align_features.\n";
+
+
+sub write_dna_align_features_to_db {
+ my ($db,$dna_align_features,$store) = @_;
+
+ DAF: foreach my $dna_align_feat (@$dna_align_features) {
+ if ($store) {
+ $db->get_DnaAlignFeatureAdaptor->store($dna_align_feat);
+ if ($@) {
+ throw("ERROR: Can't write dna_align_feat ".$dna_align_feat->hseqname." [$@]");
+ } else {
+ print "Written ".$dna_align_feat->hseqname." on chr ".$dna_align_feat->slice->name
+ ." strand ".$dna_align_feat->hstrand." with start ".$dna_align_feat->start
+ ." end ".$dna_align_feat->end."\n" if $verbose;
+ }
+ } else {
+ print "Not storing ".$dna_align_feat->hseqname."\n" if $verbose;
+ }
+ } # DAF
+ return 1;
+}
+
+sub fix_strand {
+ my $strand = shift;
+ if ($strand eq '+') {
+ $strand = 1;
+ } elsif ($strand eq '-') {
+ $strand = -1;
+ } else {
+ throw("Strand problem :".$strand);
+ }
+ return $strand;
+}
+
+sub sanity_check_cigar_line {
+ # ok, it sanity checks the GRCs idea of a cigar line which is close to GFF3 format
+ my ($line, $len) = @_;
+ my $cl_length = 0;
+ throw("Can only sanity check cigar lines with whitespace") unless $line =~ /\s/;
+ my @elements = split /\s/, $line;
+ foreach my $el (@elements) {
+ my ($operator, $num) = ($1, $2) if $el =~ /^(\w{1})(\d+)$/;
+ if ($operator =~ /[MI]/) {
+ $cl_length += $num;
+ } elsif ($operator eq 'D') {
+ # nothing to do
+ } else {
+ throw("Unknown alignment operator: $operator acting on $num");
+ }
+ }
+ if ($cl_length != $len) {
+ warn("Cigar_line length: $cl_length does not match length: $len for this line:\n$line\n\n");
+ }
+}
+
+sub reformat_cigar_line {
+ my $line = shift;
+ # hack
+ # the GRC cigar line format turns out to be back to front - fix it
+ # this is a retrospective hack, with hindsight the logic of the script
+ # would be different and probably incorporated into the sub above.
+ my @elements = split /\s/, $line;
+ $line = '';
+ foreach my $el (@elements) {
+ my ($operator, $num) = ($1, $2) if $el =~ /^(\w{1})(\d+)$/;
+ $line .= $num.$operator;
+ }
+ return $line;
+}
+
+
+exit;